Abstract
Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus, and wild rice accessions. These markers were mapped on diverse coding and non-coding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16–74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 × Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7–8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region (OsqGW5.1) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis-regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse cultivar groups) and integrated genomic strategy can efficiently scan functionally relevant potential molecular tags (markers, candidate genes and alleles) regulating complex agronomic traits (grain weight) and expedite marker-assisted genetic enhancement in rice.
Highlights
A diverse array of random and sequence-based markers such as simple sequence repeats (SSRs)/microsatellites and single nucleotide polymorphism (SNPs) developed hitherto have been successfully employed in manifold genomics-assisted breeding applications of crop plants (Kalia et al, 2011; Gupta et al, 2013; Hayward et al, 2015)
A total of 6244 in silico polymorphic SSR markers based on repeat-unit length variations among the genomic sequences of 11 accessions were developed at a genome-wide scale (Supplementary Tables S1 and S2)
An overall trend of SSR markers distribution observed in the whole rice genome based on relative density of their repeat-motif types and repeat-unit length was almost similar to that obtained within each type of non-coding and coding sequence components of rice genes (Table 1; Supplementary Figure S1B)
Summary
A diverse array of random and sequence-based markers such as simple sequence repeats (SSRs)/microsatellites and single nucleotide polymorphism (SNPs) developed hitherto have been successfully employed in manifold genomics-assisted breeding applications of crop plants (Kalia et al, 2011; Gupta et al, 2013; Hayward et al, 2015). The popularity of SSR markers can be ascribed to a number of desirable genetic attributes including co-dominant inheritance, high reproducibility, robust amplification, multiallelic nature, and wide genomic distribution in different coding and non-coding sequence components of genome (Li et al, 2004; Varshney et al, 2005; Parida et al, 2006; Miah et al, 2013) Amenability of these markers to multiplex high-throughput genotyping makes them the prime choice for various plant structural, functional and comparative genomics applications (Ashkani et al, 2011; Luo et al, 2013; Zhang et al, 2014; Kaur et al, 2015). Currently the selection of genome-wide informative SSR markers, which exhibit higher degree of polymorphism within different population groups of rice, is the most vital concern in utilization of these markers for large-scale genotyping applications and genomics-assisted crop improvement
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