Ainong Shi

University of Arkansas, Horticulture, Faculty Member

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As an associate professor at the Department of Horticulture, University of Arkansas, working on classic and molecular breeding and genetics in vegetable crops such as cowpea and spinach for cultivars and germplasm development and release

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Stephen Flower

University of Bath

HortFlora Research Spectrum

CCS University, Meerut

Anthony Melvin Crasto Ph.D

Institute of Chemical Technology, Mumbai

AJEET KUMAR

University of Delhi

Salman Ahmed

University of Karachi

Darwin H . Pangaribuan

The University Of Lampung

Y.C. Tripathi

FOREST RESEARCH INSTITUTE, DEHRADUN

Azarian Journal of Agriculture (AJA)

University of margheh

prisca a.

STIFI BHakti Pertiwi

S. Eshghi

Shiraz University

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Papers by Ainong Shi

Low frequency of the wild-type freezing-tolerance LsCBF7 allele among lettuce population suggest a negative selection during domestication and breeding

Research Square (Research Square), Jan 30, 2024

Low frequency of the wild-type freezing-tolerance LsCBF7 allele among lettuce population suggest ... more

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Genome-wide association study and genomic selection for soybean chlorophyll content associated with soybean cyst nematode tolerance

BMC Genomics, Nov 27, 2019

Background: Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, has been one of the most d... more Background: Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, has been one of the most devastating pathogens affecting soybean production. In the United States alone, SCN damage accounted for more than $1 billion loss annually. With a narrow genetic background of the currently available SCN-resistant commercial cultivars, high risk of resistance breakdown can occur. The objectives of this study were to conduct a genome-wide association study (GWAS) to identify QTL, SNP markers, and candidate genes associated with soybean leaf chlorophyll content tolerance to SCN infection, and to carry out a genomic selection (GS) study for the chlorophyll content tolerance. Results: A total of 172 soybean genotypes were evaluated for the effect of SCN HG Type 1.2.3.5.6.7 (race 4) on soybean leaf chlorophyll. The soybean lines were genotyped using a total of 4089 filtered and high-quality SNPs. Results showed that (1) a large variation in SCN tolerance based on leaf chlorophyll content indices (CCI); (2) a total of 22, 14, and 16 SNPs associated with CCI of non-SCN-infected plants, SCN-infected plants, and reduction of CCI SCN, respectively; (3) a new locus of chlorophyll content tolerance to SCN mapped on chromosome 3; (4) candidate genes encoding for Leucine-rich repeat protein, plant hormone signaling molecules, and biomolecule transporters; and (5) an average GS accuracy ranging from 0.31 to 0.46 with all SNPs and varying from 0.55 to 0.76 when GWAS-derived SNP markers were used across five models. This study demonstrated the potential of using genome-wide selection to breed chlorophyll-content-tolerant soybean for managing SCN. Conclusions: In this study, soybean accessions with higher CCI under SCN infestation, and molecular markers associated with chlorophyll content related to SCN were identified. In addition, a total of 15 candidate genes associated with chlorophyll content tolerance to SCN in soybean were also identified. These candidate genes will lead to a better understanding of the molecular mechanisms that control chlorophyll content tolerance to SCN in soybean. Genomic selection analysis of chlorophyll content tolerance to SCN showed that using significant SNPs obtained from GWAS could provide better GS accuracy.

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Impact of nutrient solutions under inorganic substrate soilless cultivation on plant growth, fruit yield and quality of tomato

Molecular Breeding in Cowpea

2014 ASHS Annual Conference, Jul 31, 2014

ABSTRACT Cowpea (Vigna unguiculata L. Walp.) (2n=2x=22) is an important and often a staple annual... more ABSTRACT Cowpea (Vigna unguiculata L. Walp.) (2n=2x=22) is an important and often a staple annual legume widely grown in Africa, Latin America, Southeast Asia, and the southern United States. It is chiefly used as a fresh or dry grain or vegetable crop for food, and can also be used as animal fodder. The objective of this project was to build a Genotyping by Sequencing (GBS) and Single Nucleotide Polymorphism (SNP) platform for molecular breeding in cowpea and to merge molecular and classical breeding to expedite genetic gain and development of new cowpea cultivars. The molecular approach includes the discovery of genome-wide SNP through GBS, analysis of genetic diversity for world-wide accessions, conducting of genome-wide association, and the identification of SNP markers associated with morphologic and agronomic traits, disease resistance, and seed quality through marker-assisted and genome-wide selection. It is expected that more than 30,000 SNPs will be discovered from 1,000 world-wide cowpea lines through GBS. Genetic diversity is being analyzed in these 1,000 cowpea lines. Genome-wide association is being conducted for morphologic traits such as plant habit, dry pod color, pod placement, mature seed pattern, seed coat color, seed pattern color, flower color, seed protein and sugar contents. Further, agronomic traits such as grain (seed) yield, 100-seed weight and seed size, along with abio- and biotic (disease and pest) resistance/tolerance to cowpea wilt (Fusarium oxysporum f. sp. tracheiphilum), cowpea mosaic virus (CPMV), bacterial blight (Xanthomonas axonopodis pv. vignicola), cowpea aphid, iron deficiency chlorosis (IDC), and low phosphorus uptake efficiency are being studied for associations. SNP markers are also being identified for these traits. This research will provide breeders a tool to select for these traits through marker-assisted selection in a cowpea breeding program.

Registration of NC97BGTD7 and NC97BGTD8 Wheat Germplasms Resistant to Powdery Mildew

Crop Science, May 1, 1999

and Ma. Saluda contains the Pm3a gene (3) and was susceptible in all greenhouse and evaluations c... more and Ma. Saluda contains the Pm3a gene (3) and was susceptible in all greenhouse and evaluations conducted in the development of the germplasms. The direct diploid to hexaploid transfer methodology followed during backcrossing was similar to that outlined by Gill and Raupp (1). We utilized A-genome diploids as donor parents in place of the D-genome diploids described in that study. The hexaploid x diploid cross, Fj embryo rescue, and development of BC,F,, BC^, and BC 2 F 2 seed were conducted during the 1988 to 1991 winter greenhouse seasons. Field selection using the pedigree breeding method was initiated with BC 2 F 2 bulk populations in the 1991-1992 season. Natural powdery mildew epiphytotics occurred each year. Selection was primarily for mildew resistance during Feekes (2) Growth Stages 8 to 10.5, but whenever possible additional selection for heading date, plant height, and straw strength was conducted using the Saluda phenotype as the benchmark. Each germplasm line traces to a single headrow harvested in 1996. Laboratory evaluations for powdery mildew resistance using the detached leaf technique were conducted during development of these germplasms and again just prior to release. Laboratory evaluations were completed with 2-cm pieces of the primary leaves floated on 0.5% water agar amended with 50 mg L~' benzimidazole and evaluated as summarized elsewhere (3). Each line was tested for homogeneity by inoculating two replicate leaf pieces from 16 plants with four distinct isolates. Line NC96BGTA6 had 3.8% susceptible offtypes, whereas NC96BGTA4 and NC96-BGTA5 were homogeneous. In addition, the three germplasms were inoculated with 30 isolates of the powdery mildew fungus with distinct differences in virulence formula and aggressiveness. These isolates had virulence to all previously identified alleles for powdery mildew resistance, with the possible exception ofPmlS. NC96BGTA4, NC96BGTA5, and NC96BGTA6 showed susceptible reactions to the 6, 0, and 1 isolates, respectively. None exhibited a susceptible reaction to commonly occurring isolates. Data and pedigree analysis showed that these germplasms contained at least one resistance gene in addition to Pm3a. Small quantities of seed (2 g) of each germplasm line are available upon written request to the corresponding author. Appropriate recognition of source should be given if this germplasm contributes to research or development of new cultivars.

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Genetical studies on the resistance of rice to Xanthomonas campestris pv. oryzae. II. Inheritance of resistance in rice to 3 strains of X. campestris pv. oryzae

Chinese Journal of Rice Science, 1990

Waterlogging during the reproductive growth stage causes physiological and biochemical modifications in the leaves of cowpea (Vigna unguiculata L.) genotypes with contrasting tolerance

Plant Physiology and Biochemistry, Nov 1, 2022

Association analysis of cowpea mosaic virus (CPMV) resistance in the USDA cowpea germplasm collection

Euphytica, Sep 7, 2017

Cowpea [Vigna unguiculata (L.) Walp.] is an important legume crop, widely grown in Africa, South ... more Cowpea [Vigna unguiculata (L.) Walp.] is an important legume crop, widely grown in Africa, South America, South Asia, Southeast Asia, and the southern United States. Cowpea is consumed as both fresh vegetable and dry grain, and as an animal feed and fodder, and it is a major dietary protein source that complements cereal-based diet. Cowpea mosaic virus (CPMV) causes a severe yield loss of cowpea in many areas worldwide notably in the Africa. Utilization of host genetic resistance is the most effective control method for the viral disease. The objective of this research is to conduct genome-wide association analysis and identify single nucleotide polymorphism (SNP) markers associated with CPMV resistance in cowpea. Three hundred and thirty-three cowpea germplasm accessions, originally collected from 39 different countries and 1033 SNPs identified from genotyping by sequencing approach were used in this study. Single marker regression, general linear model, and mixed linear model in Tassel 5 were used for association analysis of CPMV resistance. Six SNP markers (C35069548_1883, scaffold65342_6794, scaffold66293_6549, scaffold95805_2175, C350 81948_540, and scaffold17319_4417) were strongly associated with the CPMV resistance, of which the first three were associated for immune and the remaining three were associated with hypersensitive response. SNP markers identified in this research will be a potential tool to use in cowpea molecular breeding to develop CPMV resistant cultivars through marker-assisted selection.

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Genome-wide identification and expression analysis of the CBF/DREB1 gene family in lettuce

Scientific Reports, Mar 31, 2020

The C-repeat binding factor (CBF)/dehydration-responsive element binding (DREB1) proteins play a ... more The C-repeat binding factor (CBF)/dehydration-responsive element binding (DREB1) proteins play a prominent role in freezing tolerance and are highly conserved in higher plants. Here we performed a genome-wide search of the CBF/DREB1 gene family in lettuce (Lactuca sativa L.) and identified 14 members of the family with one member gene containing a nonsense mutation within the AP2 DNA-binding domain. A comprehensive phylogenetic analysis of the CBF/DREB1 family members in 20 plant species from the Asterid or Rosid clade provided evidence that tandem duplication played an important role in the expansion of the CBF/DREB1 family. Expression analysis showed that twelve of the lettuce CBF genes were responsive to low temperature (4 °C), and that three and six of them could also be responsive to salt and heat stresses, respectively. Unlike Arabidopsis thaliana whose members of the CBF/DREB1 family respond only to a particular stress, lettuce CBFs provide wider protection from combinations of abiotic stresses. A global transcriptome analysis revealed distinctive temporal expression patterns among the cold-regulated genes in lettuce plants exposed to low temperature. Genes induced throughout the cold treatment are enriched in functions associated with protection from UV and highlight intensity and the genes suppressed after 7 days of cold exposure are enriched in photosynthesis-associated functions. These results provide insight into the molecular evolutionary properties of the CBF/DREB1 gene family in lettuce and a reference for genetic improvement of the lettuce response to cold acclimation.

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Population Structure of Peronospora effusa in the Southwestern United States

PLOS ONE, Feb 1, 2016

Peronospora effusa is an obligate pathogen that causes downy mildew on spinach and is considered ... more Peronospora effusa is an obligate pathogen that causes downy mildew on spinach and is considered the most economically important disease of spinach. The objective of the current research was to assess genetic diversity of known historical races and isolates collected in 2014 from production fields in Yuma, Arizona and Salinas Valley, California. Candidate neutral single nucleotide polymorphisms (SNPs) were identified by comparing sequence data from reference isolates of known races of the pathogen collected in 2009 and 2010. Genotypes were assessed using targeted sequencing on genomic DNA extracted directly from infected plant tissue. Genotyping 26 historical and 167 contemporary samples at 46 SNP loci revealed 82 unique multi-locus genotypes. The unique genotypes clustered into five groups and the majority of isolates collected in 2014 were genetically closely related, regardless of source location. The historical samples, representing several races, showed greater genetic differentiation. Overall, the SNP data indicate much of the genotypic variation found within fields was produced during asexual development, whereas overall genetic diversity may be influenced by sexual recombination on broader geographical and temporal scales.

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Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

Research Square (Research Square), Jan 3, 2020

Background Soybean [ Glycine max (L.) Merr.] is a legume of great interest worldwide. Enhancing g... more Background Soybean [ Glycine max (L.) Merr.] is a legume of great interest worldwide. Enhancing genetic gain for agronomic traits via molecular approaches has been long considered as the main task for soybean breeders and geneticists. The objectives of this study were to evaluate maturity, plant height, seed weight, and yield in a diverse soybean accession panel, to conduct a genome-wide association study (GWAS) for these traits and identify SNP markers associated with the four traits, and to assess genomic selection (GS) accuracy. Results A total of 250 soybean accessions were evaluated for maturity, plant height, seed weight, and yield over three years. This panel was genotyped with a total of 10,259 high quality SNPs postulated from genotyping by sequencing (GBS). GWAS was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model, and GS was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that a total of 20, 31, 37, 31, and 23 SNPs were signi cantly associated with the average 3-year data for maturity, plant height, seed weight, and yield, respectively; some signi cant SNPs were mapped into previously described loci (E2 , E4 , and Dt1) affecting maturity and plant height in soybean and a new locus mapped on chromosome 20 was signi cantly associated with plant height; Glyma.10g228900 , Glyma.19g200800 , Glyma.09g196700 , and Glyma.09g038300 were candidate genes found in the vicinity of the top or the second best SNP for maturity, plant height, seed weight, and yield, respectively; a 11.5-Mb region of chromosome 10 was associated with both seed weight and yield; and GS accuracy was trait-, year-, and population structuredependent. Conclusions The SNP markers identi ed from this study for plant height, maturity, seed weight and yield can be used to improve the four agronomic traits through marker-assisted selection (MAS) and GS in soybean breeding programs. After validation, the candidate genes can be transferred to new cultivars using SNP markers through MAS. The high GS accuracy has con rmed that the four agronomic traits can be selected in molecular breeding through GS. Genome-wide association study (GWAS) and genomic selection (GS) are powerful tools to assist with understanding the genetic architecture governing complex traits of importance in agriculture. GWAS has been conducted to identify markers associated with agronomic traits in soybean (Cao et al. 2017; Yao et al. 2015). To date, more than 60 loci found through GWAS have been reported to be associated with maturity in soybean (

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Registration of NC97BGTAB9 and NC97BGTAB10 wheat germplasm lines resistant to powdery mildew

Crop Science, 2000

Evaluation of resistance to bacterial blight (Xanthomonas oryzae pv. oryzae) in wild rice species

Scientia Agricultura Sinica, 1994

A SNP-based association analysis for plant growth habit in worldwide cowpea (Vigna unguiculata (L.) Walp) Germplasm

Euphytica, Nov 22, 2017

Cowpea is a legume widely grown in Africa, North, Central and South America, and Asia. The cowpea... more Cowpea is a legume widely grown in Africa, North, Central and South America, and Asia. The cowpea plant growth habits consist of erect, semi-prostrate, and prostrate types. Developing a cultivar while considering plant growth habit is essential within a breeding program since the need for a particular growth habit is regionspecific, and significantly depends on the end user preference. Some cowpea growers might prefer erect types over semi-prostrate and prostrate types, while others would chose prostrate types, which provide more leaves for feed supplies to livestock. However, very little is known regarding the genetics of plant growth habit in cowpea to assist plant breeders in developing suitable cowpea cultivars having the desired growth habit plus the other required features. Therefore, the objectives of this study were to conduct an association mapping for cowpea growth habit, and to identify SNP markers associated with this trait. A total of 487 cowpea genotypes were evaluated for growth habit and a total of 1031 SNPs postulated from genotyping-by-sequencing to conduct association analysis study for cowpea growth habit. Our results showed that: (1) significant differences in cowpea growth habit were identified between countries, (2) the cowpea erecttype was prevalent, and (3) ten SNP markers,

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Genome Wide Association Study and Genomic Selection of Amino Acid Concentrations in Soybean Seeds

Frontiers in Plant Science, Nov 15, 2019

Soybean is a major source of protein for human consumption and animal feed. Releasing new cultiva... more Soybean is a major source of protein for human consumption and animal feed. Releasing new cultivars with high nutritional value is one of the major goals in soybean breeding. To achieve this goal, genome-wide association studies of seed amino acid contents were conducted based on 249 soybean accessions from China, US, Japan, and South Korea. The accessions were evaluated for 15 amino acids and genotyped by sequencing. Significant genetic variation was observed for amino acids among the accessions. Among the 231 single nucleotide polymorphisms (SNPs) significantly associated with variations in amino acid contents, fifteen SNPs localized near 14 candidate genes involving in amino acid metabolism. The amino acids were classified into two groups with five in one group and seven amino acids in the other. Correlation coefficients among the amino acids within each group were high and positive, but the correlation coefficients of amino acids between the two groups were negative. Twenty-five SNP markers associated with multiple amino acids can be used to simultaneously improve multi-amino acid concentration in soybean. Genomic selection analysis of amino acid concentration showed that selection efficiency of amino acids based on the markers significantly associated with all 15 amino acids was higher than that based on random markers or markers only associated with individual amino acid. The identified markers could facilitate selection of soybean varieties with improved seed quality.

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A Major Gene for Powdery Mildew Resistance Transferred to Common Wheat from Wild Einkorn Wheat

Phytopathology, Feb 1, 1998

A major gene for resistance to wheat powdery mildew (Blumeria graminis f. sp. tritici = Erysiphe ... more A major gene for resistance to wheat powdery mildew (Blumeria graminis f. sp. tritici = Erysiphe graminis f. sp. tritici) has been successfully transferred into hexaploid common wheat (Triticum aestivum, 2n = 6x = 42, AABBDD) from wild einkorn wheat (Triticum monococcum subsp. aegilopoides, 2n = 2x = 14, AA). NC96BGTA5 is a germ plasm line with the pedigree Saluda × 3/PI427662. The response patterns for powdery mildew resistance in NC96BGTA5 were tested with 30 differential isolates of B. graminis f. sp. tritici, and the line was resistant to all tested isolates. The analyses of P 1 , P 2 , F 1 , F 2 , and BC 1 F 1 populations derived from NC96BGTA5 revealed two genes for wheat powdery mildew resistance in the NC96BGTA5 line. One gene, Pm3a, was from its recurrent parent Saluda, and the second was a new gene introgressed from wild einkorn wheat. The gene was determined to be different from Pm1 to Pm21 by gene-for-gene and pedigree analyses. The new gene was identified as linked to the Pm3a gene based on the F 2 and BC 1 F 1 populations derived from a cross between NC96BGTA5 and a susceptible cultivar NK-Coker 68-15, and the data indicated that the gene was located on chromosome 1A. It is proposed that this new gene be designated Pm25 for wheat powdery mildew resistance in NC96BGTA5. Three random amplified polymorphic DNA markers, OPX06 1050 , OPAG04 950 , and OPAI14 600 , were found to be linked to this new gene. Twenty-seven major alleles have been reported at 21 loci for resistance to wheat powdery mildew (Blumeria graminis (DC.) E.O. Speer f. sp. tritici Em. Marchal = Erysiphe graminis DC. ex Merat f. sp. tritici Em. Marchal), and most of them were derived from the wild relatives of wheat (15). Because the presence and frequency of virulence genes continuously change in the B. graminis f. sp. tritici pathogen population, genes for resistance are frequently overcome by new isolates of B. graminis f. sp. tritici (7,12,14). Therefore, it will be useful to identify new resistance genes and to transfer these genes into common wheat if they are present in alien sources. Molecular markers have been widely used to tag genes for disease resistance in plants (16). Among 21 major gene loci for powdery mildew resistance in wheat, restriction fragment length polymorphism (RFLP) markers linked to Pm1, Pm2, Pm3, Pm4, Pm12, Pm13, and Pm18, and random amplified polymorphic DNA (RAPD) markers linked to Pm18 and Pm21 have been reported (3,5,6,8,13,19). Wild einkorn (Triticum monococcum L. subsp. aegilopoides (Link) Thell = T. boeoticum) (2n = 2x = 14, AA) should be a valuable source of genes for diversifying fungal disease resistance in wheat. Valkoun et al. (22) reported on reaction to leaf rust in four accessions of T. monococcum subsp. aegilopoides, and three of them were resistant. A gene, Sr22, for resistance to wheat stem rust has been successfully transferred into common wheat from T. monococcum subsp. aegilopoides (18). However, genes for wheat powdery mildew resistance have not been identified from this wild wheat relative. We recently released the common wheat germ plasm NC96BGTA5 with powdery mildew resistance transferred from the wild einkorn accession PI427662 (17). The objective of this research was to evaluate the inheritance of the resistance and to identify RAPD markers linked to the resistance gene. A preliminary report has been published (20). MATERIALS AND METHODS Plant materials. NC96BGTA5 is a new common wheat germ plasm with the pedigree Saluda × 3/PI427662 (17). PI427662 is a wild einkorn accession collected in Iraq. Saluda (PI480474) is a soft red winter wheat cultivar released in Virginia (21) that contains the Pm3a gene for resistance to wheat powdery mildew (11). Twenty differential lines (listed in Table 1) with known genes (Pm1 to Pm21, except Pm10, Pm11, Pm14, Pm15, and Pm18), the recurrent parent Saluda, and two susceptible cultivars, Chancellor and NK-Coker 68-15, were used to check response patterns in comparison with NC96BGTA5. Genes Pm10, Pm11, Pm14, and Pm15 are not effective against B. graminis f. sp. tritici (15) and were not considered here; Pm18 was unavailable. Inheritance and allelism tests. F 1 hybrid seed was obtained from crosses between NC96BGTA5 and NK-Coker 68-15, NK-Coker 9803, and Saluda (Table 2), and F 2 and BC 1 F 1 populations were developed during the 1994 to 1995 and 1995 to 1996 greenhouse seasons. Powdery mildew evaluation. Powdery mildew evaluations were performed using a detached leaf technique (11). Assessment of reaction was based on a descriptive scale of reaction types (11), in which 0 to 3 = resistant, 4 to 6 = intermediate, and 7 to 9 = susceptible. Thirty differential isolates of B. graminis f. sp. tritici were used to test response patterns of resistance to powdery mildew in NC96BGTA5. A series of lines with known powdery mildew resistance genes were also included in each test. Five B.

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A genome-wide association study and genomic prediction for Phakopsora pachyrhizi resistance in soybean

Frontiers in Plant Science, May 29, 2023

Soybean brown rust (SBR), caused by Phakopsora pachyrhizi, is a devastating fungal disease that t... more Soybean brown rust (SBR), caused by Phakopsora pachyrhizi, is a devastating fungal disease that threatens global soybean production. This study conducted a genome-wide association study (GWAS) with seven models on a panel of 3,082 soybean accessions to identify the markers associated with SBR resistance by 30,314 high quality single nucleotide polymorphism (SNPs). Then five genomic selection (GS) models, including Ridge regression best linear unbiased predictor (rrBLUP), Genomic best linear unbiased predictor (gBLUP), Bayesian least absolute shrinkage and selection operator (Bayesian LASSO), Random Forest (RF), and Support vector machines (SVM), were used to predict breeding values of SBR resistance using whole genome SNP sets and GWAS-based marker sets.

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Identification of a QTL region for ashy stem blight resistance using genome-wide association and linage analysis in common bean recombinant inbred lines derived from BAT 477 and NY6020-4

Frontiers in Plant Science, Nov 21, 2022

Ashy stem blight (ASB), caused by the fungus Macrophomina phaseolina (Tassi) Goidanich is an impo... more Ashy stem blight (ASB), caused by the fungus Macrophomina phaseolina (Tassi) Goidanich is an important disease of the common bean (Phaseolus vulgaris L.). It is important to identify quantitative trait loci (QTL) for ASB resistance and introgress into susceptible cultivars of the common bean. The objective of this research was to identify QTL and single nucleotide polymorphism (SNP) markers associated with ASB resistance in recombinant inbred lines (RIL) derived from a cross between BAT 477 and NY6020-4 common bean. One hundred and twenty-six F 6:7 RIL were phenotyped for ASB in the greenhouse. Disease severity was scored on a scale of 1-9. Genotyping was performed using whole genome resequencing with 2x common bean genome size coverage, and over six million SNPs were obtained. After being filtered, 72,017 SNPs distributed on 11 chromosomes were used to conduct the genome-wide association study (GWAS) and QTL mapping. A novel QTL region of~4.28 Mbp from 35,546,329 bp to 39,826,434 bp on chromosome Pv03 was identified for ASB resistance. The two SNPs, Chr03_39824257 and Chr03_39824268 located at 39,824,257 bp and 39,824,268 bp on Pv03, respectively, were identified as the strongest markers associated with ASB resistance. The gene Phvul.003G175900 (drought sensitive, WD repeatcontaining protein 76) located at 39,822,021-39,824,655 bp on Pv03 was Frontiers in Plant Science frontiersin.org 01

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Identification of molecular markers for Sw-5 gene of tomato spotted wilt virus resistance

American journal of biotechnology and molecular sciences, Apr 1, 2011

Tomato spotted wilt virus (TSWV) is one of the most destructive viral diseases that threaten worl... more Tomato spotted wilt virus (TSWV) is one of the most destructive viral diseases that threaten worldwide tomato (Solanuum lycopersicum L. syn Lycopersicon esculentum Mill.) production. Use of host resistance appears to be the best way to control the disease. Marker assisted selection (MAS) has become very important and useful in the selection of TSWV resistance genes. The objective of this research was to identify Sw-5 gene-specific PCR-based molecular markers and gene-derived single nucleotide polymorphism (SNP) markers for MAS in tomato breeding. A gene-specific PCR-based marker and two gene-derived SNP markers specific for TSWV resistance Sw5-b allele were identified and validated in different tomato germplasm. It is expected that the present findings will be helpful in advancing the MAS for TSWV resistance in tomato.

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Genome wide association study reveals a QTL region for ashy stem blight resistance in PRA154 Andean common bean

Plant Disease, Aug 14, 2023

Ashy stem blight (ASB) caused by Macrophomina phaseolina (Tassi) Goidanich affects common bean (P... more Ashy stem blight (ASB) caused by Macrophomina phaseolina (Tassi) Goidanich affects common bean (Phaseolus vulgaris L.) in all growing stages. Higher levels of resistance were observed in Andean common beans, but specific resistant quantitative trait loci (QTL) conferring resistance to this pathogen have not been reported in this gene pool. The objectives of this research were to: (1) conduct genome-wide association study (GWAS) and QTL mapping for resistance in the Andean breeding line PRA154, and (2) identify single nucleotide polymorphism (SNP) markers and candidate genes for ASB resistance. Phenotyping was conducted under greenhouse conditions inoculated twice with the M. phaseolina isolate PRI21 in the 107 F6:7 recombinant inbred lines (RIL) derived from the cross between the susceptible cultivar ‘Verano’ and the partial-resistant breeding line PRA154. Genotyping was performed with 109,040 SNPs distributed across all 11 P. vulgaris chromosomes. A novel major QTL was located at 28,761,668 to 31,263,845 bp extended 2.5 Mbp on chromosome Pv07 and the highest significant SNP markers were Chr07_28761668_A_G, Chr07_29131720_G_A, and Chr07_31263845_C_T with highest LOD (over 10 at most of cases) and R-squared values, explained 40 % of the phenotypic variance to PRI21 isolate. The gene Phvul.007G173900 [Methylcrotonyl-CoA carboxylase alpha chain, mitochondrial 3-methylcrotonyl-CoA carboxylase 1 (MCCA)] with the size of 10,891 bp, located at 29,131,591 to 29,142,481 bp on Pv07 was identified as one candidate for ASB resistance in PRA154 and contained Chr07_29131720_G_A. The QTL and genetic marker information could be used to assist common bean breeders to develop germplasm/cultivars with ASB resistance through molecular breeding.

Low frequency of the wild-type freezing-tolerance LsCBF7 allele among lettuce population suggest a negative selection during domestication and breeding

Research Square (Research Square), Jan 30, 2024

Low frequency of the wild-type freezing-tolerance LsCBF7 allele among lettuce population suggest ... more

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Genome-wide association study and genomic selection for soybean chlorophyll content associated with soybean cyst nematode tolerance

BMC Genomics, Nov 27, 2019

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Impact of nutrient solutions under inorganic substrate soilless cultivation on plant growth, fruit yield and quality of tomato

Molecular Breeding in Cowpea

2014 ASHS Annual Conference, Jul 31, 2014