Abstract
In the current study, we used a linkage mapping–Genome-Wide Association Study (GWAS) joint strategy to investigate quantitative trait loci (QTLs) governing rice grain shape and weight in a doubled haploid (DH) population, using Kompetitive Allele-Specific PCR (KASP) markers. Results revealed the co-detection of the QTLs, qGLE-12-1 and qGLE-12-2 (Chromosome 12), qGTE-3-1 (Chromosome 3), and qGWL-5-1 and qLWRL-5-1 (Chromosome 5), associated with grain length, width, and length–width ratio, by both linkage mapping and GWAS. In addition, qGLL-7-1 (logarithm of the odds (LOD): 18.0, late-transplanted rice) and qGLE-3-1 (LOD: 8.1, early-transplanted rice), and qLWRL-7-1 (LOD: 34.5), detected only by linkage mapping, recorded a high phenotypic variation explained (PVE) of 32.5%, 19.3%, and 37.7% for grain length, and grain length–width ratio, respectively, contributed by the allele from 93-11. Meanwhile, qGWL-5-1 (LOD: 17.2) recorded a high PVE (31.7%) for grain width, and the allele from Milyang352 contributed to the observed phenotypic variation. Furthermore, qGTL-5-1 (LOD: 21.9) had a high PVE (23.3%) for grain thickness. Similarly, qTGWE-5-1 (LOD: 8.6) showed a high contribution to the PVE for grain weight (23.4%). Moreover, QTLs, qGW-5-1, qGT-5-1, qLWR-5-1, and qTGW-5-1 coincided on chromosome 5, flanked with KJ05_17 and KJ05_13 markers. Therefore, these QTLs are suggested to govern rice grain shape and weight. Additionally, the identified candidate genes could play active roles in the regulation of rice grain shape and weight, regarding their predicted functions, and similarity with previously reported genes. Downstream breeding and functional studies are required to elucidate the roles of these candidate genes in the regulation of grain shape and weight in rice.
Highlights
For several decades, many plant breeding programs have been essentially oriented towards the development of rice varieties with high yielding potential and improved productivity [1,2,3]
Plots plots quantiles the majority trait values the predicted line, a normal indicate that of thethe majority of the fall traiton values fall on the(reference) line,suggesting suggesting distribution for grain length
Our study identified two QTLs associated with grain width in early-transplanted rice, which were mapped to chromosomes 3 and 5, the latter being detected in late-transplanted rice; whereas others, mapped to chromosomes 1, 2, 4, 8 and 10, were specific to late-transplanted rice
Summary
Many plant breeding programs have been essentially oriented towards the development of rice varieties with high yielding potential and improved productivity [1,2,3]. The interest in developing high yielding rice varieties has been sustained by the rapid increase in population. The advent of plant molecular breeding techniques and genomics approaches have contributed significantly to sustaining and accelerating the improvement of food crops, such as rice, in a relatively short time [8,9,10]. Recent advances in plant molecular breeding research and the emergence of genomics have significantly improved the understanding of the genetic contributions to the overall plant growth and development, seed formation, quality, and productivity. The use of strategic genetic approaches, such as Genome-Wide Association Studies (GWAS) [12,13,14] and OMICS [15], and the advent of genome sequencing technologies [16,17] have paved new paths towards the elucidation of the role of functional genetic components of plants underlying the phenotypic diversity and variability of complex traits between and within plant species
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