Seed shattering is an important agronomic trait in rice domestication. In this study, using a nea... more Seed shattering is an important agronomic trait in rice domestication. In this study, using a near-isogenic line (NIL-hs1) from Oryza barthii, we found a hybrid seed shattering phenomenon between the NIL-hs1 and its recurrent parent, a japonica variety Yundao 1. The heterozygotes at hybrid shattering 1 (HS1) exhibited the shattering phenotype, whereas the homozygotes from both parents conferred the non-shattering. The causal HS1 gene for hybrid shattering was located in the region between SSR marker RM17604 and RM8220 on chromosome 4. Sequence verification indicated that HS1 was identical to SH4, and HS1 controlled the hybrid shattering due to harboring the ancestral haplotype, the G allele at G237T site and C allele at C760T site from each parent. Comparative analysis at SH4 showed that all the accessions containing ancestral haplotype, including 78 wild relatives of rice and 8 African cultivated rice, had the shattering phenotype, whereas all the accessions with either of the homo...
Proceedings of the National Academy of Sciences of the United States of America, Jan 18, 2014
Comparative genomic analyses among closely related species can greatly enhance our understanding ... more Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adap...
Under different irrigation and nitrogen levels,wild rice(Oryza longistaminata) with allelopathic ... more Under different irrigation and nitrogen levels,wild rice(Oryza longistaminata) with allelopathic potential,and Oryza sativa(RD23) without allelopathic potential and their F1(RD23 × O.longistaminata) were used to study their allelopathy and weed-suppression effects to barnyard grass.During 20–50 days after transplanting,four levels of irrigation treatment,and three levels of nitrogen were conducted in the field.In bioassay,the allelopathic effect of extracting solution from rice leaves on barn-yard grass germination was observed.The results showed that O.longistaminata gave the strongest allellopathy under the condi-tions of deficiency water and low nitrogen,the inhibition rates for the root length and dry weight of barnyard grass were 69.3% and 74.6%,and decreased with elongating submerging time and increasing nitrogen.The density and biomass of barnyard grass were investigated after growing together with rice 30 days in the field.Wild rice showed the best weed-suppression effects under the alternation of wet and dry in the field.After dry cultivating for wild rice,irrigation could significantly improve its control ef-fect on barnyard grass.Furthermore,interactive effects between irrigation and nitrogen were significant on the allelopathy and weed-suppression in the field for wild rice and the F1.
To broaden the genetic basis and overcome the yield plateau in Asian cultivated rice, the exploit... more To broaden the genetic basis and overcome the yield plateau in Asian cultivated rice, the exploitation and utilization of favorable alleles from rice species with the AA genome has become important and urgent in modern breeding programs. Four different interspecific populations were used to detect quantitative trait locus (QTL) for seed length, including a BC 4 F 2 population derived from Oryza glumaepatula crossed with Dianjingyou 1 (a japonica cultivar), a BC 4 F 2 population derived from O. nivara crossed with Dianjingyou 1, a BC 7 F 1 population derived from a cross between O. longistaminata and RD23 (an indica cultivar), and a BC 8 F 1 population derived from a cross between O. glaberrima and Dianjingyou 1. The QTLs for seed length in four different populations were termed as SL-3a, SL-3b, SL-3c and SL-3d, respectively. They had good collinearity and accounted for 49% to 60% of the phenotypic variations. Sequencing data indicated that four QTLs were different alleles of GS3 which were responsible for the seed length variation between O. sativa and its four AA genome relatives. These results will be valuable for confirming the evolution of GS3 and also be helpful for rice breeding.
Hybrid sterility between Oryza glaberrima and O. sativa is a phenomenon seriously hampering the i... more Hybrid sterility between Oryza glaberrima and O. sativa is a phenomenon seriously hampering the introgression of favorable genes from each other. In order to further understand this issue, identification and isolation of hybrid sterility QTL as a single Mendelian factor are an effective strategy. A genetic map was constructed using a BC 1 F 1 population derived from a cross between an O. sativa japonica cultivar and an O. glaberrima accession. Four main-effect QTLs for pollen sterility were detected in the BC 1 F 1. Five BC 8 F 1 advanced backcross populations were developed via successive backcrosses based on phenotype and molecular selections. The BC 8 F 1 populations showed bimodal distribution for pollen fertility and could be classified into semi-sterile and fertile types, fitting single Mendilian factor inheritance ratios. Three QTLs detected in BC 1 F 1 corresponding to qSS-3, qSS-6a and qSS-7 were mapped on chromosomes 6, 3 and 7, respectively, as single Mendilian factors.
To tackle food insecurity faced by an ever-growing population, there is an urgent need to develop... more To tackle food insecurity faced by an ever-growing population, there is an urgent need to develop new forms of highly productive and ecologically-secure agricultural systems. Crop perennialization provides a novel and promising solution to both food security and environmental challenges. Compared with annual grain production systems, which often undermine basic ecosystem services, perennial crops could maintain important ecosystem functions and reduce agricultural inputs. Here, we report our successful breeding of perennial rice (PR) taking over 20 years. We introduced perennial growth into domesticated Asian rice by interspecific hybridization and subsequently developed several perennial cultivars that have been commercialized recently in China and successfully trialed in multiple countries. The perennial cultivars produce yields comparable to commercialized annual rice (AR) varieties and maintain them for 4-5 consecutive years from a single planting. They exhibit robust regrowth, ...
Two SNP Mutations Turned off Seed Shattering in Rice, 2023
Seed shattering is an important agronomic trait in rice domestication. In this study, using a nea... more Seed shattering is an important agronomic trait in rice domestication. In this study, using a near-isogenic line (NIL-hs1) from Oryza barthii, we found a hybrid seed shattering phenomenon between the NIL-hs1 and its recurrent parent, a japonica variety Yundao 1. The heterozygotes at hybrid shattering 1 (HS1) exhibited the shattering phenotype, whereas the homozygotes from both parents conferred the non-shattering. The causal HS1 gene for hybrid shattering was located in the region between SSR marker RM17604 and RM8220 on chromosome 4. Sequence verification indicated that HS1 was identical to SH4, and HS1 controlled the hybrid shattering due to harboring the ancestral haplotype, the G allele at G237T site and C allele at C760T site from each parent. Comparative analysis at SH4 showed that all the accessions containing ancestral haplotype, including 78 wild relatives of rice and 8 African cultivated rice, had the shattering phenotype, whereas all the accessions with either of the homozygous domestic haplotypes at one of the two sites, including 17 wild relatives of rice, 111 African cultivated rice and 65 Asian cultivated rice, showed the non-shattering phenotype. Dominant complementation of the G allele at G237T site and the C allele at C760T site in HS1 led to a hybrid shattering phenotype. These results help to shed light on the nature of seed shattering in rice during domestication and improve the moderate shattering varieties adapted to mechanized harvest.
Seed shattering is an important agronomic trait in rice domestication. In this study, using a nea... more Seed shattering is an important agronomic trait in rice domestication. In this study, using a near-isogenic line (NIL-hs1) from Oryza barthii, we found a hybrid seed shattering phenomenon between the NIL-hs1 and its recurrent parent, a japonica variety Yundao 1. The heterozygotes at hybrid shattering 1 (HS1) exhibited the shattering phenotype, whereas the homozygotes from both parents conferred the non-shattering. The causal HS1 gene for hybrid shattering was located in the region between SSR marker RM17604 and RM8220 on chromosome 4. Sequence verification indicated that HS1 was identical to SH4, and HS1 controlled the hybrid shattering due to harboring the ancestral haplotype, the G allele at G237T site and C allele at C760T site from each parent. Comparative analysis at SH4 showed that all the accessions containing ancestral haplotype, including 78 wild relatives of rice and 8 African cultivated rice, had the shattering phenotype, whereas all the accessions with either of the homo...
Proceedings of the National Academy of Sciences of the United States of America, Jan 18, 2014
Comparative genomic analyses among closely related species can greatly enhance our understanding ... more Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adap...
Under different irrigation and nitrogen levels,wild rice(Oryza longistaminata) with allelopathic ... more Under different irrigation and nitrogen levels,wild rice(Oryza longistaminata) with allelopathic potential,and Oryza sativa(RD23) without allelopathic potential and their F1(RD23 × O.longistaminata) were used to study their allelopathy and weed-suppression effects to barnyard grass.During 20–50 days after transplanting,four levels of irrigation treatment,and three levels of nitrogen were conducted in the field.In bioassay,the allelopathic effect of extracting solution from rice leaves on barn-yard grass germination was observed.The results showed that O.longistaminata gave the strongest allellopathy under the condi-tions of deficiency water and low nitrogen,the inhibition rates for the root length and dry weight of barnyard grass were 69.3% and 74.6%,and decreased with elongating submerging time and increasing nitrogen.The density and biomass of barnyard grass were investigated after growing together with rice 30 days in the field.Wild rice showed the best weed-suppression effects under the alternation of wet and dry in the field.After dry cultivating for wild rice,irrigation could significantly improve its control ef-fect on barnyard grass.Furthermore,interactive effects between irrigation and nitrogen were significant on the allelopathy and weed-suppression in the field for wild rice and the F1.
To broaden the genetic basis and overcome the yield plateau in Asian cultivated rice, the exploit... more To broaden the genetic basis and overcome the yield plateau in Asian cultivated rice, the exploitation and utilization of favorable alleles from rice species with the AA genome has become important and urgent in modern breeding programs. Four different interspecific populations were used to detect quantitative trait locus (QTL) for seed length, including a BC 4 F 2 population derived from Oryza glumaepatula crossed with Dianjingyou 1 (a japonica cultivar), a BC 4 F 2 population derived from O. nivara crossed with Dianjingyou 1, a BC 7 F 1 population derived from a cross between O. longistaminata and RD23 (an indica cultivar), and a BC 8 F 1 population derived from a cross between O. glaberrima and Dianjingyou 1. The QTLs for seed length in four different populations were termed as SL-3a, SL-3b, SL-3c and SL-3d, respectively. They had good collinearity and accounted for 49% to 60% of the phenotypic variations. Sequencing data indicated that four QTLs were different alleles of GS3 which were responsible for the seed length variation between O. sativa and its four AA genome relatives. These results will be valuable for confirming the evolution of GS3 and also be helpful for rice breeding.
Hybrid sterility between Oryza glaberrima and O. sativa is a phenomenon seriously hampering the i... more Hybrid sterility between Oryza glaberrima and O. sativa is a phenomenon seriously hampering the introgression of favorable genes from each other. In order to further understand this issue, identification and isolation of hybrid sterility QTL as a single Mendelian factor are an effective strategy. A genetic map was constructed using a BC 1 F 1 population derived from a cross between an O. sativa japonica cultivar and an O. glaberrima accession. Four main-effect QTLs for pollen sterility were detected in the BC 1 F 1. Five BC 8 F 1 advanced backcross populations were developed via successive backcrosses based on phenotype and molecular selections. The BC 8 F 1 populations showed bimodal distribution for pollen fertility and could be classified into semi-sterile and fertile types, fitting single Mendilian factor inheritance ratios. Three QTLs detected in BC 1 F 1 corresponding to qSS-3, qSS-6a and qSS-7 were mapped on chromosomes 6, 3 and 7, respectively, as single Mendilian factors.
To tackle food insecurity faced by an ever-growing population, there is an urgent need to develop... more To tackle food insecurity faced by an ever-growing population, there is an urgent need to develop new forms of highly productive and ecologically-secure agricultural systems. Crop perennialization provides a novel and promising solution to both food security and environmental challenges. Compared with annual grain production systems, which often undermine basic ecosystem services, perennial crops could maintain important ecosystem functions and reduce agricultural inputs. Here, we report our successful breeding of perennial rice (PR) taking over 20 years. We introduced perennial growth into domesticated Asian rice by interspecific hybridization and subsequently developed several perennial cultivars that have been commercialized recently in China and successfully trialed in multiple countries. The perennial cultivars produce yields comparable to commercialized annual rice (AR) varieties and maintain them for 4-5 consecutive years from a single planting. They exhibit robust regrowth, ...
Two SNP Mutations Turned off Seed Shattering in Rice, 2023
Seed shattering is an important agronomic trait in rice domestication. In this study, using a nea... more Seed shattering is an important agronomic trait in rice domestication. In this study, using a near-isogenic line (NIL-hs1) from Oryza barthii, we found a hybrid seed shattering phenomenon between the NIL-hs1 and its recurrent parent, a japonica variety Yundao 1. The heterozygotes at hybrid shattering 1 (HS1) exhibited the shattering phenotype, whereas the homozygotes from both parents conferred the non-shattering. The causal HS1 gene for hybrid shattering was located in the region between SSR marker RM17604 and RM8220 on chromosome 4. Sequence verification indicated that HS1 was identical to SH4, and HS1 controlled the hybrid shattering due to harboring the ancestral haplotype, the G allele at G237T site and C allele at C760T site from each parent. Comparative analysis at SH4 showed that all the accessions containing ancestral haplotype, including 78 wild relatives of rice and 8 African cultivated rice, had the shattering phenotype, whereas all the accessions with either of the homozygous domestic haplotypes at one of the two sites, including 17 wild relatives of rice, 111 African cultivated rice and 65 Asian cultivated rice, showed the non-shattering phenotype. Dominant complementation of the G allele at G237T site and the C allele at C760T site in HS1 led to a hybrid shattering phenotype. These results help to shed light on the nature of seed shattering in rice during domestication and improve the moderate shattering varieties adapted to mechanized harvest.
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