QTL mapping using an ultra-high-density SNP map reveals a major locus for grain yield in an elite rice restorer R998

Abstract

To dissect the genetic basis of yield formation in restorer line of hybrid rice, we conducted QTL analysis for 6 yield traits including panicles per plant (PPP), grains per panicle (GPP), grain yield per plant (GY), thousand-grain weight (TGW), above-ground biomass (AGB), and harvest index (HI) using SNP markers in a recombinant inbred lines (RILs) population derived from a cross between a tropical japonica inbred Francis and an elite indica restorer Guanghui 998 (R998). A total of 26 QTLs were detected using a high density genetic map consisting of 3016 bin markers. Nineteen out of the 26 QTL alleles from R998 had a beneficial effect on yield traits. Most of the QTLs were co-located with previously reported rice QTLs. qAGB6 and qHI9, controlling AGB and HI respectively, were detected as novel QTLs. Four QTLs for GY were repeatedly detected across two years, with all the beneficial alleles from R998. Notably, qGY8 explained over 20% of the yield variance in both years. Moreover, qGY8 together with qTGW8 and qHI8 formed a QTL cluster. Markers tightly linked with qGY8 were developed. Cloning of qGY8 will facilitate its further exploitation in high-yield breeding.

Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population

“…Our study is a first report for exploring genetic architecture of grain yield and grain quality through the combination of association and pedigree-based studies in 16-way MAGIC rice population although several studies reported for yield and grain quality traits 1,3,4,8,9,11–13 . Many published studies mentioned that most of high-yielding varieties have longer growth duration for longer metabolic activities and grain filling 41 .…”

“…The production of rice has been significantly improved after the development of semi-dwarf cultivars and hybrid rice 3 . However, in the last decades, rice yield was not significantly improved and reached into a projected rice production 4 . To ensure food security, declining in genetic gain, narrow genetic base of the modern rice varieties, biotic and abiotic stress pressure, increasing demand for more quantity and better quality of rice are some of the concerns for rice breeders 2,3,5 .…”

Finding new QTL for yield traits based on a high-density genetic map in the super hybrid rice Nei2You No.6

“…Bin map refers to a certain number of continuous SNP as the unit for determining recombination events, and the parent source of each Bin is speculated to obtain the genome-wide physical map of the offspring. For example, a high-density genetic map consisting of 3016 bin was constructed and finally 26 QTL for six yield traits were located, among which two novel QTL, qAGB6 and qHI9, were identified [20]. In another report, a total of 79 QTL for 15 yield traits were mapped using a high-density linkage map with 3569 bin markers [21].…”

Genome‐wide SNP discovery and QTL mapping for economic traits in a recombinant inbred line of Oryza sativa

“…Tang and colleagues characterized the genome‐wide SNPs of the parental varieties of recombinant inbred line (RIL) populations using the high‐throughput GBS and identified a QTL containing the locus Os4g48460 (a putative cytochrome P450) related to rice seed size (Tang et al, 2016). Zhu performed QTL mapping in a restorer line of hybrid rice based on ultra‐high‐density SNP mapping and found 26 QTLs for six yield traits, in which nine QTL alleles presented a significant effect (Zhu et al, 2017). Jiang performed the high‐density genetic map in the QTL mapping of 124 rice backcrossed recombinant inbred lines and showed six QTLs related to seed germination in response to the cold stress (Jiang et al, 2017).…”