Genomewide discovery ofDNApolymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance

Abstract

SummaryNext-generation sequencing technologies provide opportunities to understand the genetic basis of phenotypic differences, such as abiotic stress response, even in the closely related cultivars via identification of large number of DNA polymorphisms. We performed wholegenome resequencing of three rice cultivars with contrasting responses to drought and salinity stress (sensitive IR64, drought-tolerant Nagina 22 and salinity-tolerant Pokkali). More than 356 million 90-bp paired-end reads were generated, which provided about 85% coverage of the rice genome. Applying stringent parameters, we identified a total of 1 784 583 nonredundant single-nucleotide polymorphisms (SNPs) and 154 275 InDels between reference (Nipponbare) and the three resequenced cultivars. We detected 401 683 and 662 509 SNPs between IR64 and Pokkali, and IR64 and N22 cultivars, respectively. The distribution of DNA polymorphisms was found to be uneven across and within the rice chromosomes. One-fourth of the SNPs and InDels were detected in genic regions, and about 3.5% of the total SNPs resulted in nonsynonymous changes. Large-effect SNPs and InDels, which affect the integrity of the encoded protein, were also identified. Further, we identified DNA polymorphisms present in the differentially expressed genes within the known quantitative trait loci. Among these, a total of 548 SNPs in 232 genes, located in the conserved functional domains, were identified. The data presented in this study provide functional markers and promising target genes for salinity and drought tolerance and present a valuable resource for high-throughput genotyping and molecular breeding for abiotic stress traits in rice.

Whole Genome Sequencing and Analysis of Godawee, a Salt Tolerant Indica Rice Variety

“…The reads covered 91.65% of the reference genome. In agreement with previous reports of similar genome wide studies of other rice varieties 8.35% of the reads did not map to the reference genome [41,42]. Further analysis of the unmapped reads showed that the reads consisted of sequences which mapped to other Oryza sativa subspecies as has been reported previously [43].…”

Molecular characterization of edible pea through EST-SSR markers

“…Belaj et al (2003) reported that SSR markers show the highest level of polymorphism compared to RAPD and AFLP in olive. The same results were reported in various other studies where SSR markers were compared to other molecular markers (Jain et al, 2014). Therefore, SSRs have increasingly become the marker set of choice for genetic studies as they are abundant, highly polymorphic, codominant in nature, and genome-specific (Cuevas and Prom, 2013;Izzah et al, 2013).…”

“…Different stresses are constant threats to the field pea and the key to pea improvement programs is to have genetic variation for agronomically important traits within the parental lines that are used in crosses for maximizing the genetic gain (Taran et al, 2005). For this purpose, assessment of genetic diversity between germplasm/ varieties to utilize their protection, conservation, and registration is also used in breeding programs to provide the bulk of allelic variation in breeding material (Jain et al, 2014).…”

“…Therefore, molecular markers are the means to overcome the limitations associated with these markers (Rao, 2004) as estimation of genetic diversity through molecular markers is independent of environmental influences (Tatikonda et al, 2009). Various molecular markers such as intersimple sequence repeat (ISSR) (Zietkiewiez et al, 1994), sequence-related amplified polymorphism (SRAP) (Li and Quiros, 2001), single nucleotide polymorphism (SNP) (Jain et al, 2014), amplified fragment-length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), and simple sequence repeats (SSR) markers are predominantly used for molecular characterization in plants (Belaj et al, 2003).…”

“…The effectiveness of these different DNA markers has been employed in several plant species (Jain et al, 2014). Belaj et al (2003) reported that SSR markers show the highest level of polymorphism compared to RAPD and AFLP in olive.…”