Genetic Dissection of Seed Dormancy using Chromosome Segment Substitution Lines in Rice (Oryza sativa L.)

Abstract

Timing of germination determines whether a new plant life cycle can be initiated; therefore, appropriate dormancy and rapid germination under diverse environmental conditions are the most important features for a seed. However, the genetic architecture of seed dormancy and germination behavior remains largely elusive. In the present study, a linkage analysis for seed dormancy and germination behavior was conducted using a set of 146 chromosome segment substitution lines (CSSLs), of which each carries a single or a few chromosomal segments of Nipponbare (NIP) in the background of Zhenshan 97 (ZS97). A total of 36 quantitative trait loci (QTLs) for six germination parameters were identified. Among them, qDOM3.1 was validated as a major QTL for seed dormancy in a segregation population derived from the qDOM3.1 near-isogenic line, and further delimited into a genomic region of 90 kb on chromosome 3. Based on genetic analysis and gene expression profiles, the candidate genes were restricted to eight genes, of which four were responsive to the addition of abscisic acid (ABA). Among them, LOC_Os03g01540 was involved in the ABA signaling pathway to regulate seed dormancy. The results will facilitate cloning the major QTLs and understanding the genetic architecture for seed dormancy and germination in rice and other crops.

A genome‐wide association study reveals that the 2‐oxoglutarate/malate translocator mediates seed vigor in rice

“…The four QTLs were designated as qGR3.1, qGR3.2 (both located on chromosome 3), qGR8 (chromosome 8), and qGR11 (chromosome 11) (Figure 1b). The regions of qGR3.1 and qGR3.2 were similar to previous QTLs identified for seed dormancy (Cai and Morishima, 2000;Wan et al, 2006;Yuan et al, 2020), and the QTLs qGR8 and qGR11 had regions similar to QTLs for seed germination under normal and low temperature conditions, respectively (Jiang et al, 2006;Wang et al, 2010b; Figure 1c). Interestingly, the lowest P-value existed in the region of qGR11, implying that it is a major QTL for germination rate, and this was further investigated.…”

Genome-Wide Association Study for Seed Dormancy Using Re-Sequenced Germplasm under Multiple Conditions in Rice

“…To date, hundreds of QTLs associated with seed dormancy in rice have been reported, mainly through linkage mapping using biparental populations in cultivated, wild and weedy rice. The QTL mapping of other traits in rice populations including recombinant inbred lines (RILs), F 2 and chromosome segment substitution lines (CSSLs) is commonly used [ 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. Among them, a few QTLs have been finely mapped, such as Sdr1 [ 30 ], qLTG3-1 [ 26 ], qSD12 [ 31 ], qSDn-1 [ 20 ], qSDn-5 [ 20 ], qSD7-1 [ 27 ], qSD10 [ 32 ], qDOM3.1 [ 28 ], qSdr9 [ 33 ] and qSD6 [ 22 ].…”

“…The QTL mapping of other traits in rice populations including recombinant inbred lines (RILs), F 2 and chromosome segment substitution lines (CSSLs) is commonly used [ 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. Among them, a few QTLs have been finely mapped, such as Sdr1 [ 30 ], qLTG3-1 [ 26 ], qSD12 [ 31 ], qSDn-1 [ 20 ], qSDn-5 [ 20 ], qSD7-1 [ 27 ], qSD10 [ 32 ], qDOM3.1 [ 28 ], qSdr9 [ 33 ] and qSD6 [ 22 ]. Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) is a powerful method to identify marker-trait associations (MTAs) without creating artificial mapping populations and has been used in dissecting the genetic basis of complex traits including seed dormancy.…”

Rice Genetics: Trends and Challenges for the Future Crops Production

“…The pyramiding lines developed using five bacterial blight resistance genes (xa4, xa5, xa7, xa13, xa21) showed not only high levels of resistance to bacterial blight disease, but also improved grain quantity and quality [29]. In addition, many researchers have isolated and functionally characterized salinity and osmosis-related genes (DEP1, qLTG3-1, OsSAP16, qDOM3.1, OsWRKY, and OsCIPK) to significantly improve grain yield and quality [30][31][32]. To date, the great progress has been achieved in uncovering the mechanisms of how rice senses and responds to external nutrients [33].…”