World collection of sorghum consists of 235,711 accessions, housed in national and international ... more World collection of sorghum consists of 235,711 accessions, housed in national and international genebanks, of which, ICRISAT genebank holds 37,949 accessions, predominantly landraces from SAT regions. Biologically, this collection represents all basic and intermediate races, and geographic regions. Core/mini core, genotype-based reference set or in some cases trait-based diversity panels have been developed. These reduced subsets are in demand to discover new sources of variation, dissect population structure and diversity, estimate linkage disequilibria, map marker-trait associations, and mine allelic variations associated with agronomically benefi cial traits. More emphasis should also be to discover germplasm with novel seed quality traits imparting health benefi ts. Few germplasm, such as IS 18758, IS 1054, and IS 33844, have proved to be an excellent source of desirable plant type, high grain yield, good grain quality, resistant to leaf diseases, and used extensively in breeding programs at ICRISAT and elsewhere. New sources such Genetic Resources,
This book and the individual contributions contained in it are protected under copyright by the P... more This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein). Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary. Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility.
Symbiotic nitrogen fixation (SNF) is a sustainable alternative for nitrogen supply for plants in ... more Symbiotic nitrogen fixation (SNF) is a sustainable alternative for nitrogen supply for plants in agriculture. Past efforts to enhance SNF in chickpea through inoculation with improved rhizobia were partially successful. Hence, there is an urgent need to identify nodulation variants among the mini-core and races accessions of chickpea. In the present study, a total of 211 mini-core lines, 68 land races and 3 checks were evaluated for nodulation variants under greenhouse conditions at ICRISAT, Patancheru, India and IIPR, Kanpur, India. The seeds of all accessions were inoculated with IC-76, a nodulating bacteria, on both locations. When the potting material was pasteurized, the organic carbon had reduced from 0.49% to 0.29% whereas no significant difference was noted in total N and available P contents. At 45 days after sowing, the mini-core lines of chickpea were categorized into 6 types, based on nodulation capability (rating 0-5, where 0=no nodules; while 5 = maximum nodules) at bo...
Zero hunger and good health could be realized by 2030 through effective conservation, characteriz... more Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicerarietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite ge...
Frequent utilization of wild Cicer species in chickpea (Cicer arietinum L.) improvement programs,... more Frequent utilization of wild Cicer species in chickpea (Cicer arietinum L.) improvement programs, as well as the regeneration of these wild species for efficient conservation in genebanks, is hindered due to photoperiod and/or temperature sensitivity (vernalization). In this study, the response to four extended photoperiod treatments (15, 18, 21, and 24 h) was compared with a control (12 h) for phenology and growth in terms of reduction in number of days to first flowering, as well as for yield‐related traits in cultivated chickpea and seven annual wild Cicer species. The study revealed that wild Cicer species required long photoperiods (varying from 15 to 18 h) for transition from the vegetative to reproductive phase. Optimum photoperiods also improved agronomic traits such as pod number and seed yield per plant. Of the photoperiods studied, 18 h was the most appropriate photoperiod treatment for both reducing the vegetative phase and for efficient regeneration in C. reticulatum La...
Ploidy difference between wild Arachis species and cultivated genotypes hinder transfer of useful... more Ploidy difference between wild Arachis species and cultivated genotypes hinder transfer of useful alleles for agronomically important traits. To overcome this genetic barrier, two synthetic tetraploids, viz., ISATGR 1212 (A. duranensis ICG 8123 × A. ipaensis ICG 8206) and ISATGR 265-5A (A. kempff-mercadoi ICG 8164 × A. hoehnei ICG 8190), were used to generate two advanced backcross (AB) populations. The AB-populations, namely, AB-pop1 (ICGV 91114 × ISATGR 1212) and AB-pop2, (ICGV 87846 × ISATGR 265-5A) were genotyped with DArT and SSR markers. Genetic maps were constructed for AB-pop1 and AB-pop2 populations with 258 loci (1415.7 cM map length and map density of 5.5 cM/loci) and 1043 loci (1500.8 cM map length with map density of 1.4 cM/loci), respectively. Genetic analysis identified large number of wild segments in the population and provided a good source of diversity in these populations. Phenotyping of these two populations identified several introgression lines with good agronomic, oil quality, and disease resistance traits. Quantitative trait locus (QTL) analysis showed that the wild genomic segments contributed favourable alleles for foliar disease resistance while cultivated genomic segments mostly contributed favourable alleles for oil quality and yield component traits. These populations, after achieving higher stability, will be useful resource for genetic mapping and QTL discovery for wild species segments in addition to using population progenies in breeding program for diversifying the gene pool of cultivated groundnut.
In the past five decades, constant research has been directed towards yield improvement in pigeon... more In the past five decades, constant research has been directed towards yield improvement in pigeonpea resulting in the deployment of several commercially acceptable cultivars in India. Though, the genesis of hybrid technology, the biggest breakthrough, enigma of stagnant productivity still remains unsolved. To sort this productivity disparity, genomic research along with conventional breeding was successfully initiated at ICRISAT. It endowed ample genomic resource providing insight in the pigeonpea genome combating production constraints in a precise and speedy manner. The availability of the draft genome sequence with a large-scale marker resource, oriented the research towards trait mapping for flowering time, determinacy, fertility restoration, yield attributing traits and photo-insensitivity. Defined core and mini-core collection, still eased the pigeonpea breeding being accessible for existing genetic diversity and developing stress resistance. Modern genomic tools like next-generation sequencing, genome-wide selection helping in the appraisal of selection efficiency is leading towards next-generation breeding, an awaited milestone in pigeonpea genetic enhancement. This paper emphasizes the ongoing genetic improvement in pigeonpea with an amalgam of conventional breeding as well as genomic research.
Our agricultural system and hence food security is threatened by combination of events, such as i... more Our agricultural system and hence food security is threatened by combination of events, such as increasing population, the impacts of climate change and the need to a more sustainable development. Evolutionary adaptation may help some species to overcome environmental changes through new selection pressures driven by climate change. However, success of evolutionary adaptation is dependent on various factors, one of which is the extent of genetic variation available within species. Genomic approaches provide an exceptional opportunity to identify genetic variation that can be employed in crop improvement programs. In this review, we illustrate some of the routinely used genomics-based methods as well as recent breakthroughs, which facilitate assessment of genetic variation and discovery of adaptive genes in legumes. While additional information is needed, the current utility of selection tools indicate a robust ability to utilize existing variation among legumes to address the challe...
Indian Journal of Genetics and Plant Breeding (The), 2016
Pigeonpea (Cajanus cajan (L.) Millspaugh) is an important grain legume grown in tropical and subt... more Pigeonpea (Cajanus cajan (L.) Millspaugh) is an important grain legume grown in tropical and subtropical regions of the world. Narrow genetic base coupled with low levels of resistance against important biotic/abiotic stresses in cultivated pigeonpea is the major constraint affecting its production and productivity globally. Wild Cajanus species are the reservoir of many important genes including resistance/tolerance to diseases, insect-pests and drought, and good agronomic traits and can be utilized to improve the crop cultivars, enrich variability, and broaden the genetic base. Utilization of wild Cajanus species has contributed for the development of cytoplasmic male sterility (CMS) systems for pigeonpea improvement. Prebreeding populations involving promising wild Cajanus accessions belonging to secondary and tertiary gene pools as donors and popular pigeonpea cultivars as recipients were developed for enriching variability for pigeonpea improvement. Considerable variability was observed in these populations for morpho-agronomic traits and for biotic stresses. Two advanced backcross populations derived from wild Cajanus species are being genotyped to identify QTLs associated with agronomic traits for further deployment in pigeonpea improvement programs. Agronomically desirable and disease resistant introgression lines have been identified and shared with breeding programs for developing new high-yielding and climateresilient pigeonpea cultivars with a broad genetic base.
Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers... more Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.
All rights reserved. No part of this periodical may be reproduced or transmitted in any form or b... more All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher.
Accelerating plant breeding Centromere-mediated genome elimination Genetic transformation and and... more Accelerating plant breeding Centromere-mediated genome elimination Genetic transformation and androgenesis Haploids and doubled haploids In vitro gametic tissues and plant breeding The discovery of haploids in higher plants led to the use of doubled haploid (DH) technology in plant breeding. This article provides the state of the art on DH technology including the induction and identification of haploids, what factors influence haploid induction, molecular basis of microspore embryogenesis, the genetics underpinnings of haploid induction and its use in plant breeding, particularly to fix traits and unlock genetic variation. Both in vitro and in vivo methods have been used to induce haploids that are thereafter chromosome doubled to produce DH. Various heritable factors contribute to the successful induction of haploids, whose genetics is that of a quantitative trait. Genomic regions associated with in vitro and in vivo DH production were noted in various crops with the aid of DNA markers. It seems that F 2 plants are the most suitable for the induction of DH lines than F 1 plants. Identifying putative haploids is a key issue in haploid breeding. DH technology in Brassicas and cereals, such as barley, maize, rice, rye and wheat, has been improved and used routinely in cultivar development, while in other food staples such as pulses and root crops the technology has not reached to the stage leading to its application in plant breeding. The centromere-mediated haploid induction system has been used in Arabidopsis, but not yet in crops. Most food staples are derived from genomic resources-rich crops, including those with sequenced reference genomes. The integration of genomic resources with DH technology provides new opportunities for the improving selection methods, maximizing selection gains and accelerate cultivar development. Marker-aided breeding and DH technology have been used to improve host plant resistance in barley, rice, and wheat. Multinational seed companies are using DH technology in large-scale production of inbred lines for further development of hybrid cultivars, particularly in maize. The public sector provides support to national programs or small-medium private seed for the exploitation of DH technology in plant breeding.
ABSTRACTDowny mildew (DM), caused by Sclerospora graminicola (Sacc.) Schröt., is a highly destruc... more ABSTRACTDowny mildew (DM), caused by Sclerospora graminicola (Sacc.) Schröt., is a highly destructive and widespread disease in most pearl millet [Pennisetum glaucum (L.) R. Br.] growing areas of Asia and Africa. Breeding for DM resistance continues to be an integral part of genetic improvement of pearl millet at ICRISAT, Patancheru, India. For the identification of new and diverse sources of DM resistance, a pearl millet mini core collection comprising 238 accessions was screened against eight pathotypes (Sg 384, Sg 409, Sg 445, Sg 457, Sg 510, Sg 519, Sg 526, and Sg 542) of S. graminicola collected from different geographical locations in India. Significant differences for DM reaction were observed among pathotypes, mini core accessions, and their interactions. Of the 238 accessions, 68 accessions were resistant (≤10% DM incidence) to pathotype Sg 510 followed by 40 accessions resistant to Sg 457. Resistance to pathotypes Sg 519, Sg 526, Sg 384, Sg 445, and Sg 542 was observed in ...
Symbiotic nitrogen fixation (SNF) in root nodules of grain legumes such as chickpea is a highly c... more Symbiotic nitrogen fixation (SNF) in root nodules of grain legumes such as chickpea is a highly complex process that drastically affects the gene expression patterns of both the prokaryotic as well as eukaryotic interacting cells. A successfully established symbiotic relationship requires mutual signaling mechanisms and a continuous adaptation of the metabolism of the involved cells to varying environmental conditions. Although some of these processes are well understood today many of the molecular mechanisms underlying SNF, especially in chickpea, remain unclear. Here, we reannotated our previously published transcriptome data generated by deepSuperSAGE (Serial Analysis of Gene Expression) to the recently published draft genome of chickpea to assess the root-and nodule-specific transcriptomes of the eukaryotic host cells. The identified gene expression patterns comprise up to 71 significantly differentially expressed genes and the expression of twenty of these was validated by quantitative real-time PCR with the tissues from five independent biological replicates. Many of the differentially expressed transcripts were found to encode proteins implicated in sugar metabolism, antioxidant defense as well as biotic and abiotic stress responses of the host cells, and some of them were already known to contribute to SNF in other legumes. The differentially expressed genes identified in this study represent candidates that can be used for further characterization of the complex molecular mechanisms underlying SNF in chickpea.
Peanut is an important and nutritious agricultural commodity and a livelihood of many smallholder... more Peanut is an important and nutritious agricultural commodity and a livelihood of many smallholder farmers in the semi-arid tropics (SAT) of world which are facing serious production threats. Integration of genomics tools with ongoing genetic improvement approaches is expected to facilitate accelerated development of improved cultivars. Therefore, highresolution genotyping and multiple season phenotyping data for 50 important agronomic, disease and quality traits were generated on the 'reference set' of peanut. This study reports comprehensive analyses of allelic diversity, population structure, linkage disequilibrium (LD) decay and marker-trait association (MTA) in peanut. Distinctness of all the genotypes can be established by using either an unique allele detected by a single SSR or a combination of unique alleles by two or more than two SSR markers. As expected, DArT features (2.0 alleles/locus, 0.125 PIC) showed lower allele frequency and polymorphic information content (PIC) than SSRs (22.21 alleles /locus, 0.715 PIC). Both marker types clearly differentiated the genotypes of diploids from tetraploids. Multi-allelic SSRs identified three subgroups (K = 3) while the LD simulation trend line based on squared-allele frequency correlations (r 2) predicted LD decay of 15-20 cM in peanut genome. Detailed analysis identified a total of 524 highly significant MTAs (pvalue .2.1610-6) with wide phenotypic variance (PV) range (5.81-90.09%) for 36 traits. These MTAs after validation may be deployed in improving biotic resistance, oil/ seed/ nutritional quality, drought tolerance related traits, and yield/ yield components.
Plant height and maturity are two critical traits in sorghum breeding. To develop molecular tools... more Plant height and maturity are two critical traits in sorghum breeding. To develop molecular tools and to identify genes underlying the traits for molecular breeding, we developed 14,739 SNP markers used to genotype the complete sorghum [Sorghum bicolor (L.) Moench] mini core collection. The collection was evaluated in four rainy and three post-rainy season environments for plant height and maturity. Association analysis identified six marker loci linked to height and ten to maturity in at least two environments with at least two SNPs in each locus. Of these, 14 were in close proximity to previously mapped height/maturity QTL in sorghum. Candidate genes for maturity or plant height close to the marker loci include a sugar transporter (SbSUC9), an auxin response factor (SbARF3), an FLC and FT regulator (SbMED12), and a photoperiod response gene (SbPPR1) for maturity and peroxidase 53, and an auxin transporter (SbLAX4) for plant height. Linkage disequilibrium analysis showed that SbPPR1 and SbARF3 were in regions with reduced sequence variation among early-maturing accessions, suggestive of past purifying selection. We also found a linkage disequilibrium block that existed only among the accessions with short plant height in rainy season environments. The block contains a gene homologous to the Arabidopsis flowering time gene, LUMINIDEPENDENS (LD). Functional LD promotes early maturity while mutation delays maturity, affecting plant height. Previous studies also found reduced sequence variations within this gene. These newly-mapped SNP markers will facilitate further efforts to identify plant height or maturity genes in sorghum. H. D. Upadhyaya and Y.-H. Wang have contributed equally to this work.
Anthracnose in sorghum caused by Colletotrichum sublineolum is one of the most destructive diseas... more Anthracnose in sorghum caused by Colletotrichum sublineolum is one of the most destructive diseases affecting sorghum production under warm and humid conditions. Markers and genes linked to resistance to the disease are important for plant breeding. Using 14,739 SNP markers, we have mapped eight loci linked to resistance in sorghum through association analysis of a sorghum minicore collection consisting of 242 diverse accessions evaluated for anthracnose resistance for 2 years in the field. The mini-core was representative of the International Crops Research Institute for the Semi-Arid Tropics' worldwide sorghum landrace collection. Eight marker loci were associated with anthracnose resistance in both years. Except locus 8, disease resistance-related genes were found in all loci based on their physical distance from linked SNP markers. These include two NB-ARC class of R genes on chromosome 10 that were partially homologous to the rice blast resistance gene Pib, two hypersensitive responserelated genes: autophagy-related protein 3 on chromosome 1 and 4 harpin-induced 1 (Hin1) homologs on chromosome 8, a RAV transcription factor that is also part of R gene pathway, an oxysterol-binding protein that functions in the non-specific host resistance, and homologs of menthone:neomenthol reductase (MNR) that catalyzes a menthone reduction to produce the antimicrobial neomenthol. These genes and markers may be developed into molecular tools for genetic improvement of anthracnose resistance in sorghum. Communicated by I. Godwin.
This article appeared in a journal published by Elsevier. The attached copy is furnished to the a... more This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright
World collection of sorghum consists of 235,711 accessions, housed in national and international ... more World collection of sorghum consists of 235,711 accessions, housed in national and international genebanks, of which, ICRISAT genebank holds 37,949 accessions, predominantly landraces from SAT regions. Biologically, this collection represents all basic and intermediate races, and geographic regions. Core/mini core, genotype-based reference set or in some cases trait-based diversity panels have been developed. These reduced subsets are in demand to discover new sources of variation, dissect population structure and diversity, estimate linkage disequilibria, map marker-trait associations, and mine allelic variations associated with agronomically benefi cial traits. More emphasis should also be to discover germplasm with novel seed quality traits imparting health benefi ts. Few germplasm, such as IS 18758, IS 1054, and IS 33844, have proved to be an excellent source of desirable plant type, high grain yield, good grain quality, resistant to leaf diseases, and used extensively in breeding programs at ICRISAT and elsewhere. New sources such Genetic Resources,
This book and the individual contributions contained in it are protected under copyright by the P... more This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein). Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary. Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility.
Symbiotic nitrogen fixation (SNF) is a sustainable alternative for nitrogen supply for plants in ... more Symbiotic nitrogen fixation (SNF) is a sustainable alternative for nitrogen supply for plants in agriculture. Past efforts to enhance SNF in chickpea through inoculation with improved rhizobia were partially successful. Hence, there is an urgent need to identify nodulation variants among the mini-core and races accessions of chickpea. In the present study, a total of 211 mini-core lines, 68 land races and 3 checks were evaluated for nodulation variants under greenhouse conditions at ICRISAT, Patancheru, India and IIPR, Kanpur, India. The seeds of all accessions were inoculated with IC-76, a nodulating bacteria, on both locations. When the potting material was pasteurized, the organic carbon had reduced from 0.49% to 0.29% whereas no significant difference was noted in total N and available P contents. At 45 days after sowing, the mini-core lines of chickpea were categorized into 6 types, based on nodulation capability (rating 0-5, where 0=no nodules; while 5 = maximum nodules) at bo...
Zero hunger and good health could be realized by 2030 through effective conservation, characteriz... more Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicerarietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite ge...
Frequent utilization of wild Cicer species in chickpea (Cicer arietinum L.) improvement programs,... more Frequent utilization of wild Cicer species in chickpea (Cicer arietinum L.) improvement programs, as well as the regeneration of these wild species for efficient conservation in genebanks, is hindered due to photoperiod and/or temperature sensitivity (vernalization). In this study, the response to four extended photoperiod treatments (15, 18, 21, and 24 h) was compared with a control (12 h) for phenology and growth in terms of reduction in number of days to first flowering, as well as for yield‐related traits in cultivated chickpea and seven annual wild Cicer species. The study revealed that wild Cicer species required long photoperiods (varying from 15 to 18 h) for transition from the vegetative to reproductive phase. Optimum photoperiods also improved agronomic traits such as pod number and seed yield per plant. Of the photoperiods studied, 18 h was the most appropriate photoperiod treatment for both reducing the vegetative phase and for efficient regeneration in C. reticulatum La...
Ploidy difference between wild Arachis species and cultivated genotypes hinder transfer of useful... more Ploidy difference between wild Arachis species and cultivated genotypes hinder transfer of useful alleles for agronomically important traits. To overcome this genetic barrier, two synthetic tetraploids, viz., ISATGR 1212 (A. duranensis ICG 8123 × A. ipaensis ICG 8206) and ISATGR 265-5A (A. kempff-mercadoi ICG 8164 × A. hoehnei ICG 8190), were used to generate two advanced backcross (AB) populations. The AB-populations, namely, AB-pop1 (ICGV 91114 × ISATGR 1212) and AB-pop2, (ICGV 87846 × ISATGR 265-5A) were genotyped with DArT and SSR markers. Genetic maps were constructed for AB-pop1 and AB-pop2 populations with 258 loci (1415.7 cM map length and map density of 5.5 cM/loci) and 1043 loci (1500.8 cM map length with map density of 1.4 cM/loci), respectively. Genetic analysis identified large number of wild segments in the population and provided a good source of diversity in these populations. Phenotyping of these two populations identified several introgression lines with good agronomic, oil quality, and disease resistance traits. Quantitative trait locus (QTL) analysis showed that the wild genomic segments contributed favourable alleles for foliar disease resistance while cultivated genomic segments mostly contributed favourable alleles for oil quality and yield component traits. These populations, after achieving higher stability, will be useful resource for genetic mapping and QTL discovery for wild species segments in addition to using population progenies in breeding program for diversifying the gene pool of cultivated groundnut.
In the past five decades, constant research has been directed towards yield improvement in pigeon... more In the past five decades, constant research has been directed towards yield improvement in pigeonpea resulting in the deployment of several commercially acceptable cultivars in India. Though, the genesis of hybrid technology, the biggest breakthrough, enigma of stagnant productivity still remains unsolved. To sort this productivity disparity, genomic research along with conventional breeding was successfully initiated at ICRISAT. It endowed ample genomic resource providing insight in the pigeonpea genome combating production constraints in a precise and speedy manner. The availability of the draft genome sequence with a large-scale marker resource, oriented the research towards trait mapping for flowering time, determinacy, fertility restoration, yield attributing traits and photo-insensitivity. Defined core and mini-core collection, still eased the pigeonpea breeding being accessible for existing genetic diversity and developing stress resistance. Modern genomic tools like next-generation sequencing, genome-wide selection helping in the appraisal of selection efficiency is leading towards next-generation breeding, an awaited milestone in pigeonpea genetic enhancement. This paper emphasizes the ongoing genetic improvement in pigeonpea with an amalgam of conventional breeding as well as genomic research.
Our agricultural system and hence food security is threatened by combination of events, such as i... more Our agricultural system and hence food security is threatened by combination of events, such as increasing population, the impacts of climate change and the need to a more sustainable development. Evolutionary adaptation may help some species to overcome environmental changes through new selection pressures driven by climate change. However, success of evolutionary adaptation is dependent on various factors, one of which is the extent of genetic variation available within species. Genomic approaches provide an exceptional opportunity to identify genetic variation that can be employed in crop improvement programs. In this review, we illustrate some of the routinely used genomics-based methods as well as recent breakthroughs, which facilitate assessment of genetic variation and discovery of adaptive genes in legumes. While additional information is needed, the current utility of selection tools indicate a robust ability to utilize existing variation among legumes to address the challe...
Indian Journal of Genetics and Plant Breeding (The), 2016
Pigeonpea (Cajanus cajan (L.) Millspaugh) is an important grain legume grown in tropical and subt... more Pigeonpea (Cajanus cajan (L.) Millspaugh) is an important grain legume grown in tropical and subtropical regions of the world. Narrow genetic base coupled with low levels of resistance against important biotic/abiotic stresses in cultivated pigeonpea is the major constraint affecting its production and productivity globally. Wild Cajanus species are the reservoir of many important genes including resistance/tolerance to diseases, insect-pests and drought, and good agronomic traits and can be utilized to improve the crop cultivars, enrich variability, and broaden the genetic base. Utilization of wild Cajanus species has contributed for the development of cytoplasmic male sterility (CMS) systems for pigeonpea improvement. Prebreeding populations involving promising wild Cajanus accessions belonging to secondary and tertiary gene pools as donors and popular pigeonpea cultivars as recipients were developed for enriching variability for pigeonpea improvement. Considerable variability was observed in these populations for morpho-agronomic traits and for biotic stresses. Two advanced backcross populations derived from wild Cajanus species are being genotyped to identify QTLs associated with agronomic traits for further deployment in pigeonpea improvement programs. Agronomically desirable and disease resistant introgression lines have been identified and shared with breeding programs for developing new high-yielding and climateresilient pigeonpea cultivars with a broad genetic base.
Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers... more Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.
All rights reserved. No part of this periodical may be reproduced or transmitted in any form or b... more All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher.
Accelerating plant breeding Centromere-mediated genome elimination Genetic transformation and and... more Accelerating plant breeding Centromere-mediated genome elimination Genetic transformation and androgenesis Haploids and doubled haploids In vitro gametic tissues and plant breeding The discovery of haploids in higher plants led to the use of doubled haploid (DH) technology in plant breeding. This article provides the state of the art on DH technology including the induction and identification of haploids, what factors influence haploid induction, molecular basis of microspore embryogenesis, the genetics underpinnings of haploid induction and its use in plant breeding, particularly to fix traits and unlock genetic variation. Both in vitro and in vivo methods have been used to induce haploids that are thereafter chromosome doubled to produce DH. Various heritable factors contribute to the successful induction of haploids, whose genetics is that of a quantitative trait. Genomic regions associated with in vitro and in vivo DH production were noted in various crops with the aid of DNA markers. It seems that F 2 plants are the most suitable for the induction of DH lines than F 1 plants. Identifying putative haploids is a key issue in haploid breeding. DH technology in Brassicas and cereals, such as barley, maize, rice, rye and wheat, has been improved and used routinely in cultivar development, while in other food staples such as pulses and root crops the technology has not reached to the stage leading to its application in plant breeding. The centromere-mediated haploid induction system has been used in Arabidopsis, but not yet in crops. Most food staples are derived from genomic resources-rich crops, including those with sequenced reference genomes. The integration of genomic resources with DH technology provides new opportunities for the improving selection methods, maximizing selection gains and accelerate cultivar development. Marker-aided breeding and DH technology have been used to improve host plant resistance in barley, rice, and wheat. Multinational seed companies are using DH technology in large-scale production of inbred lines for further development of hybrid cultivars, particularly in maize. The public sector provides support to national programs or small-medium private seed for the exploitation of DH technology in plant breeding.
ABSTRACTDowny mildew (DM), caused by Sclerospora graminicola (Sacc.) Schröt., is a highly destruc... more ABSTRACTDowny mildew (DM), caused by Sclerospora graminicola (Sacc.) Schröt., is a highly destructive and widespread disease in most pearl millet [Pennisetum glaucum (L.) R. Br.] growing areas of Asia and Africa. Breeding for DM resistance continues to be an integral part of genetic improvement of pearl millet at ICRISAT, Patancheru, India. For the identification of new and diverse sources of DM resistance, a pearl millet mini core collection comprising 238 accessions was screened against eight pathotypes (Sg 384, Sg 409, Sg 445, Sg 457, Sg 510, Sg 519, Sg 526, and Sg 542) of S. graminicola collected from different geographical locations in India. Significant differences for DM reaction were observed among pathotypes, mini core accessions, and their interactions. Of the 238 accessions, 68 accessions were resistant (≤10% DM incidence) to pathotype Sg 510 followed by 40 accessions resistant to Sg 457. Resistance to pathotypes Sg 519, Sg 526, Sg 384, Sg 445, and Sg 542 was observed in ...
Symbiotic nitrogen fixation (SNF) in root nodules of grain legumes such as chickpea is a highly c... more Symbiotic nitrogen fixation (SNF) in root nodules of grain legumes such as chickpea is a highly complex process that drastically affects the gene expression patterns of both the prokaryotic as well as eukaryotic interacting cells. A successfully established symbiotic relationship requires mutual signaling mechanisms and a continuous adaptation of the metabolism of the involved cells to varying environmental conditions. Although some of these processes are well understood today many of the molecular mechanisms underlying SNF, especially in chickpea, remain unclear. Here, we reannotated our previously published transcriptome data generated by deepSuperSAGE (Serial Analysis of Gene Expression) to the recently published draft genome of chickpea to assess the root-and nodule-specific transcriptomes of the eukaryotic host cells. The identified gene expression patterns comprise up to 71 significantly differentially expressed genes and the expression of twenty of these was validated by quantitative real-time PCR with the tissues from five independent biological replicates. Many of the differentially expressed transcripts were found to encode proteins implicated in sugar metabolism, antioxidant defense as well as biotic and abiotic stress responses of the host cells, and some of them were already known to contribute to SNF in other legumes. The differentially expressed genes identified in this study represent candidates that can be used for further characterization of the complex molecular mechanisms underlying SNF in chickpea.
Peanut is an important and nutritious agricultural commodity and a livelihood of many smallholder... more Peanut is an important and nutritious agricultural commodity and a livelihood of many smallholder farmers in the semi-arid tropics (SAT) of world which are facing serious production threats. Integration of genomics tools with ongoing genetic improvement approaches is expected to facilitate accelerated development of improved cultivars. Therefore, highresolution genotyping and multiple season phenotyping data for 50 important agronomic, disease and quality traits were generated on the 'reference set' of peanut. This study reports comprehensive analyses of allelic diversity, population structure, linkage disequilibrium (LD) decay and marker-trait association (MTA) in peanut. Distinctness of all the genotypes can be established by using either an unique allele detected by a single SSR or a combination of unique alleles by two or more than two SSR markers. As expected, DArT features (2.0 alleles/locus, 0.125 PIC) showed lower allele frequency and polymorphic information content (PIC) than SSRs (22.21 alleles /locus, 0.715 PIC). Both marker types clearly differentiated the genotypes of diploids from tetraploids. Multi-allelic SSRs identified three subgroups (K = 3) while the LD simulation trend line based on squared-allele frequency correlations (r 2) predicted LD decay of 15-20 cM in peanut genome. Detailed analysis identified a total of 524 highly significant MTAs (pvalue .2.1610-6) with wide phenotypic variance (PV) range (5.81-90.09%) for 36 traits. These MTAs after validation may be deployed in improving biotic resistance, oil/ seed/ nutritional quality, drought tolerance related traits, and yield/ yield components.
Plant height and maturity are two critical traits in sorghum breeding. To develop molecular tools... more Plant height and maturity are two critical traits in sorghum breeding. To develop molecular tools and to identify genes underlying the traits for molecular breeding, we developed 14,739 SNP markers used to genotype the complete sorghum [Sorghum bicolor (L.) Moench] mini core collection. The collection was evaluated in four rainy and three post-rainy season environments for plant height and maturity. Association analysis identified six marker loci linked to height and ten to maturity in at least two environments with at least two SNPs in each locus. Of these, 14 were in close proximity to previously mapped height/maturity QTL in sorghum. Candidate genes for maturity or plant height close to the marker loci include a sugar transporter (SbSUC9), an auxin response factor (SbARF3), an FLC and FT regulator (SbMED12), and a photoperiod response gene (SbPPR1) for maturity and peroxidase 53, and an auxin transporter (SbLAX4) for plant height. Linkage disequilibrium analysis showed that SbPPR1 and SbARF3 were in regions with reduced sequence variation among early-maturing accessions, suggestive of past purifying selection. We also found a linkage disequilibrium block that existed only among the accessions with short plant height in rainy season environments. The block contains a gene homologous to the Arabidopsis flowering time gene, LUMINIDEPENDENS (LD). Functional LD promotes early maturity while mutation delays maturity, affecting plant height. Previous studies also found reduced sequence variations within this gene. These newly-mapped SNP markers will facilitate further efforts to identify plant height or maturity genes in sorghum. H. D. Upadhyaya and Y.-H. Wang have contributed equally to this work.
Anthracnose in sorghum caused by Colletotrichum sublineolum is one of the most destructive diseas... more Anthracnose in sorghum caused by Colletotrichum sublineolum is one of the most destructive diseases affecting sorghum production under warm and humid conditions. Markers and genes linked to resistance to the disease are important for plant breeding. Using 14,739 SNP markers, we have mapped eight loci linked to resistance in sorghum through association analysis of a sorghum minicore collection consisting of 242 diverse accessions evaluated for anthracnose resistance for 2 years in the field. The mini-core was representative of the International Crops Research Institute for the Semi-Arid Tropics' worldwide sorghum landrace collection. Eight marker loci were associated with anthracnose resistance in both years. Except locus 8, disease resistance-related genes were found in all loci based on their physical distance from linked SNP markers. These include two NB-ARC class of R genes on chromosome 10 that were partially homologous to the rice blast resistance gene Pib, two hypersensitive responserelated genes: autophagy-related protein 3 on chromosome 1 and 4 harpin-induced 1 (Hin1) homologs on chromosome 8, a RAV transcription factor that is also part of R gene pathway, an oxysterol-binding protein that functions in the non-specific host resistance, and homologs of menthone:neomenthol reductase (MNR) that catalyzes a menthone reduction to produce the antimicrobial neomenthol. These genes and markers may be developed into molecular tools for genetic improvement of anthracnose resistance in sorghum. Communicated by I. Godwin.
This article appeared in a journal published by Elsevier. The attached copy is furnished to the a... more This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright
Uploads
Papers by Hari Upadhyaya