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

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.

Genomic Breeding of Green Super Rice Varieties and Their Deployment in Asia and Africa

“…The system was used for genotypic identification of the pedigree and derivative pedigree materials of a superior rice variety, Huanghuazhan (HHZ) for GSR development. As a result, a total of 1113 conserved and traceable chromosomal regions were identified, including genes related to many important agronomic traits, such as sd1 (controlling plant height), Ehd4 (controlling heading date), htd1 (controlling tiller height and dwarfing), SSIIa (controlling soluble starch synthesis), GS3 (controlling grain size), Amy3A (controlling amylase), Gn1a (controlling grain number), and TAC1 (controlling tillering angle) (Zhou et al 2016a;Chen et al 2017).…”

Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang

“…Based on a group of SNPs, a number of improvement‐selective sweeps involving a string of causal genes and IBD segments inherited from foundation parents have been identified, laying a foundation for germplasm resource analysis and breeding by design in the future. In recent years, an abundance studies have been performed to trace IBD segments and exploit key trait regions during the breeding process following their well‐defined genetic paths (Chen et al , ; Fang et al , ; Lai et al , ; Lu et al , ; Ma et al , ; Wu et al , ). Based on more than 2 million SNPs, the Xinjiang cotton population could be divided into two groups (Figure ), preliminarily indicating that Upland cotton populations in Xinjiang were not only spawned from DPL15, STV2B and UGDM, which are the original germplasms used for modern Upland cotton breeding in Yangtze River and Yellow River cotton‐growing regions in China (Fang et al , ), but also have a close kinship with the former Soviet Union cotton landraces.…”

“…Moreover, identity‐by‐descent (IBD) regions have been demonstrated to be powerful in relatedness evaluation and mapping of genetic loci associated with phenotypic variations in many studies (Browning and Browning, ; Browning and Thompson, ; Stevens et al , ; Westerlind et al , ) . The shift in genomic structure and the history of the genetic architecture of Huanghuazhan have been analysed, and the major effectual genomic regions were pinpointed to traceable genomic regions (Chen et al , ; Zhou et al , ). In addition, Fang et al () used IBD detection to show that the genetic contributions of Deltapline 15 (DPL15), Stoneville 2B (STV2B) and Uganda cotton (UGDM) to seven widely grown cultivars in China were approximately 14.19%, 10.45% and 4.19%, respectively.…”

Resequencing core accessions of a pedigree identifies derivation of genomic segments and key agronomic trait loci during cotton improvement

“…Using the appropriate molecular markers, we can now comprehensively analyse the genetic makeup and track the derivation through detection of traceable identity by descent (IBD) fragments, which are genomic segments inherited from their ancestral parents (Fang et al ., ; Wu et al ., ). In addition, pedigree‐based selective sweep analysis is also able to reveal selective signatures that have arisen during modern crop improvement and identify genomic regions related to artificial selection (Chen et al ., ; Doebley et al ., ).…”

“…Moreover, genome‐wide resequencing also provides an opportunity for genetic analysis of the backbone parents and for studying the rapid recombination of genomic segments in a conformed relationship pedigree during crop breeding (Wu et al ., ). For example, according to combined pedigree and SNP information, the shift of genomic structure and history of genetic architecture during breeding improvement of Huanghuazhan, a famous rice backbone parent, were revealed, and the major effectual genomic regions were pinpointed to the derivation of traceable genomic blocks (Chen et al ., ; Zhou et al ., ). Based on pedigree resequencing, Lai et al .…”