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CUBIC: an atlas of genetic architecture promises directed maize improvement

 Identifying genotype-phenotype links and causative genes from quantitative trait loci (QTL) is challenging for complex agronomically important traits. To accelerate maize gene discovery and breeding, we present the Complete-diallel design plus Unbalanced Breeding-like Inter-Cross (CUBIC) population, consisting of 1404 individuals created by extensively inter-crossing 24 widely used Chinese maize founders. Results: Hundreds of QTL for 23 agronomic traits are uncovered with 14 million high-quality SNPs and a high-resolution identity-by-descent map, which account for an average of 75% of the heritability for each trait.

Hai-Jun LiuXiaqing WangYingjie XiaoJingyun LuoFeng QiaoWenyu YangRuyang ZhangYijiang MengJiamin SunShijuan YanYong PengLuyao NiuLiumei JianWei SongJiali YanChunhui LiYanxin ZhaoYa LiuMarilyn L WarburtonJiuran ZhaoJianbing Yan.

 

Genome Biol. 2020 Jan 24;21(1):20.

 

Background: Identifying genotype-phenotype links and causative genes from quantitative trait loci (QTL) is challenging for complex agronomically important traits. To accelerate maize gene discovery and breeding, we present the Complete-diallel design plus Unbalanced Breeding-like Inter-Cross (CUBIC) population, consisting of 1404 individuals created by extensively inter-crossing 24 widely used Chinese maize founders.

 

Results: Hundreds of QTL for 23 agronomic traits are uncovered with 14 million high-quality SNPs and a high-resolution identity-by-descent map, which account for an average of 75% of the heritability for each trait. We find epistasis contributes to phenotypic variance widely. Integrative cross-population analysis and cross-omics mapping allow effective and rapid discovery of underlying genes, validated here with a case study on leaf width.

 

Conclusions: Through the integration of experimental genetics and genomics, our study provides useful resources and gene mining strategies to explore complex quantitative traits.

 

See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6979394/

 

Development of the CUBIC population. The present CUBIC population, consisting of 1404 progenies, was derived from 24 elite Chinese maize inbred lines. a These 24 founders were crossed under a Complete Diallel Cross type IV (CDC IV) mating design, omitting parents and reciprocal crosses. Thirty F1s with best agronomic performance (early flowering time, small ear height, and big ear size) were selected to further cross in the CDC IV design. b Another 110 F1s were randomly selected for open pollination in isolation. Two hundred and 400 ears were harvested from the agronomically selected and randomly selected subsets, respectively, and seeds from the above F1s were mixed together in a 2:1 ratio with the expectation of improving population performance and maximizing diversity. c The resulting individuals were planted under open pollination in isolation for 6 generations. About 2000 ears of the most diverse lines were retained and mixed equally in each generation. Finally, the population was self-pollinated by single seed descent for another 6 generations, and a total of 1664 inbred lines were obtained, of which 1404 have been successfully sampled and sequenced, and thus used in further analysis.

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