Shaoxia
Chen^1,2,*, Zechuan Lin^1,*, Degui Zhou³,
Chongrong Wang³, Hong Li³, Renbo Yu¹, Hanchao
Deng⁴, Xiaoyan Tang^4,5, Shaochuan Zhou³, Xing
Wang Deng^1,2 & Hang He^1,2

Scientific Reports

DOI: 10.1038/srep45685

Abstract

Improving
breeding has been widely utilized in crop breeding and contributed to yield and
quality improvement, yet few researches have been done to analyze genetic
architecture underlying breeding improvement comprehensively. Here, we
collected genotype and phenotype data of 99 cultivars from the complete
pedigree including Huanghuazhan, an elite, high-quality, conventional indica
rice that has been grown over 4.5 million hectares in southern China and from
which more than 20 excellent cultivars have been derived. We identified 1,313
selective sweeps (SSWs) revealing four stage-specific selection patterns
corresponding to improvement preference during 65 years, and 1113 conserved Huanghuazhan
traceable blocks (cHTBs) introduced from different donors and conserved in
>3 breeding generations were the core genomic regions for superior
performance of Huanghuazhan. Based on 151 quantitative trait loci (QTLs)
identified for 13 improved traits in the pedigree, we reproduced their
improvement process in silico, highlighting improving breeding works well for
traits controlled by major/major + minor effect QTLs, but was inefficient for
traits controlled by QTLs with complex interactions or explaining low levels of
phenotypic variation. These results indicate long-term breeding improvement is
efficient to construct superior genetic architecture for elite performance, yet
molecular breeding with designed genotype of QTLs can facilitate complex traits
improvement.

附件：Genome-wide study of an elite rice pedigree reveals a complex history of genetic architecture for breeding improvement