Fan Zhang1,2, Conghe Zhang3, Xiuqin Zhao1, Shuangbing Zhu4, Kai Chen4, Guixiang Zhou3, Zhichao Wu1, Min Li2, Tianqing Zheng1, Wensheng Wang1,2, Zhi Yan3, Qinyong Fei3, Zhikang Li5,6,7, Jinjie Chen8, Jianlong Xu9,10. 1. Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. 2. College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China. 3. Winall Hi-Tech Seed Co., Ltd., Hefei, 230088, Anhui, China. 4. Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China. 5. Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. zhkli1953@126.com. 6. College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China. zhkli1953@126.com. 7. Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China. zhkli1953@126.com. 8. Winall Hi-Tech Seed Co., Ltd., Hefei, 230088, Anhui, China. m13505601533@163.com. 9. Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. xujlcaas@126.com. 10. Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China. xujlcaas@126.com.
Abstract
BACKGROUND: Since its development and wide adoption in China, hybrid rice has reached the yield plateau for more than three decades. To understand the genetic basis of heterosis in rice and accelerate hybrid rice breeding, the yield performances of the elite rice hybrid, Quan-you-si-miao (QYSM) were genetically dissected by whole-genome sequencing, large-scale phenotyping of 1061 recombined inbred lines (RILs) and 1061 backcross F1 (BCF1) hybrids derived from QYSM's parents across three environments and gene-based analyses. RESULTS: Genome-wide scanning of 13,847 segregating genes between the parents and linkage mapping based on 855 bins across the rice genome and phenotyping experiments across three environments resulted in identification of large numbers of genes, 639 main-effect QTLs (M-QTLs) and 2736 epistatic QTLs with significant additive or heterotic effects on the trait performances of the combined population consisting of RILs and BCF1 hybrids, most of which were environment-specific. The 324 M-QTLs affecting yield components included 32.7% additive QTLs, 38.0% over-dominant or dominant ones with strong and positive effects and 29.3% under-dominant or incomplete recessive ones with significant negative heterotic effects. 63.6% of 1403 genes with allelic introgression from subspecies japonica/Geng in the parents of QYSM may have contributed significantly to the enhanced yield performance of QYSM. CONCLUSIONS: The parents of QYSM and related rice hybrids in China carry disproportionally more additive and under-dominant genes/QTLs affecting yield traits. Further focus in indica/Xian rice breeding should shift back to improving inbred varieties, while breaking yield ceiling of Xian hybrids can be achieved by one or combinations of the three strategies: (1) by pyramiding favorable alleles of additive genes, (2) by eliminating or minimizing under-dominant loci, and (3) by pyramiding overdominant/dominant genes polymorphic, particularly those underlying inter-subspecific heterosis.
BACKGROUND: Since its development and wide adoption in China, hybrid rice has reached the yield plateau for more than three decades. To understand the genetic basis of heterosis in rice and accelerate hybrid rice breeding, the yield performances of the elite rice hybrid, Quan-you-si-miao (QYSM) were genetically dissected by whole-genome sequencing, large-scale phenotyping of 1061 recombined inbred lines (RILs) and 1061 backcross F1 (BCF1) hybrids derived from QYSM's parents across three environments and gene-based analyses. RESULTS: Genome-wide scanning of 13,847 segregating genes between the parents and linkage mapping based on 855 bins across the rice genome and phenotyping experiments across three environments resulted in identification of large numbers of genes, 639 main-effect QTLs (M-QTLs) and 2736 epistatic QTLs with significant additive or heterotic effects on the trait performances of the combined population consisting of RILs and BCF1 hybrids, most of which were environment-specific. The 324 M-QTLs affecting yield components included 32.7% additive QTLs, 38.0% over-dominant or dominant ones with strong and positive effects and 29.3% under-dominant or incomplete recessive ones with significant negative heterotic effects. 63.6% of 1403 genes with allelic introgression from subspecies japonica/Geng in the parents of QYSM may have contributed significantly to the enhanced yield performance of QYSM. CONCLUSIONS: The parents of QYSM and related rice hybrids in China carry disproportionally more additive and under-dominant genes/QTLs affecting yield traits. Further focus in indica/Xian rice breeding should shift back to improving inbred varieties, while breaking yield ceiling of Xian hybrids can be achieved by one or combinations of the three strategies: (1) by pyramiding favorable alleles of additive genes, (2) by eliminating or minimizing under-dominant loci, and (3) by pyramiding overdominant/dominant genes polymorphic, particularly those underlying inter-subspecific heterosis.
Authors: James A Birchler; Hong Yao; Sivanandan Chudalayandi; Daniel Vaiman; Reiner A Veitia Journal: Plant Cell Date: 2010-07-09 Impact factor: 11.277
Authors: Ryo Fujimoto; Kosuke Uezono; Sonoko Ishikura; Kenji Osabe; W James Peacock; Elizabeth S Dennis Journal: Breed Sci Date: 2018-04-12 Impact factor: 2.086