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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #333403

Research Project: Development and Application of Genetic, Genomic, and Bioinformatic Resources in Maize

Location: Plant, Soil and Nutrition Research

Title: Analysis of recombination QTLs, segregation distortion, and epistasis for fitness in maize multiple populations using ultra-high-density markers

Author
item Li, Chunhui - Chinese Academy Of Agricultural Sciences
item Li, Yongxiang - Chinese Academy Of Agricultural Sciences
item Shi, Yunsu - Chinese Academy Of Agricultural Sciences
item Song, Yanchun - Chinese Academy Of Agricultural Sciences
item Zhang, Dengfeng - Chinese Academy Of Agricultural Sciences
item Buckler, Edward - Ed
item Zhang, Zhiwu - Cornell University - New York
item Li, Yu - Chinese Academy Of Agricultural Sciences
item Wang, Tianyu - Chinese Academy Of Agricultural Sciences

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/4/2016
Publication Date: 7/5/2016
Citation: Li, C., Li, Y., Shi, Y., Song, Y., Zhang, D., Buckler IV, E.S., Zhang, Z., Li, Y., Wang, T. 2016. Analysis of recombination QTLs, segregation distortion, and epistasis for fitness in maize multiple populations using ultra-high-density markers. Theoretical and Applied Genetics. 129(9):1775-1784.

Interpretive Summary: In genetics, normally the offspring equally inherit from each of their parents. However, when these simple rules of genetics are not observed understanding the basis of inheritance can provide important insights to complex genomes. By combining the two largest public diversity panels in maize, this study was able to evaluate these distortions in inheritance. In general, maize show very little distortion relative to other crop species. However, regions of the genome with extensive recombination (chromosome mixing) exhibit the expected parental inheritances, while those regions of the genome with little recombination show large distortions. This is likely the result of a buildup of deleterious mutations in these regions of the genome. In addition, natural variation in pollen factors also produced consistent distortions. These results provide insights in how crossing and breeding can be optimized for maize.

Technical Abstract: Understanding the maize genomic features would be useful for the study of genetic diversity and evolution and for maize breeding. Here, we used two maize nested association mapping (NAM) populations separately derived in China (CN-NAM) and the US (US-NAM) to explore the maize genomic features. The two populations containing 36 families and about 7000 recombinant inbred lines were evaluated with genotyping-by-sequencing. Through the comparison between the two NAMs, we revealed that segregation distortion is little, whereas epistasis for fitness is present in the two maize NAM populations. When conducting quantitative trait loci (QTL) mapping for the total number of recombination events, we detected 14 QTLs controlling recombination. Using high-density markers to identify segregation distortion regions (SDRs), a total of 445 SDRs were detected within the 36 families, among which 15 common SDRs were found in at least ten families. About 80% of the known maize gametophytic factors (ga) genes controlling segregation distortion were overlapped with highly significant SDRs. In addition, we also found that the regions with high recombination rate and high gene density usually tended to have little segregation distortion. This study will facilitate population genetic studies and gene cloning affecting recombination variation and segregation distortion in maize, which can improve plant breeding progress.