Genetic analysis for rice grain quality traits in the YVB stable variant line using RAD-seq

Abstract

The future of rice breeding will likely be built on the basis of the further utilization of heterosis between elite cultivars and genetic resources from distant subspecies of rice. Previous studies have proved that exogenous genomic DNA transformation methods can be used to transfer genetic information from distant relatives (donor) into cultivated rice (recipient). However, the mechanism underlying this form of genetic transfer is poorly characterized, and the genes that cause the phenotypic changes in these variants are typically difficult to identify. This study examined YVB, a stable variant line with greatly improved grain quality traits that was derived from an indica variety (V20B) by transferring genomic DNA of O.minuta through the "spike-stalk injection method (SIM)". We used restriction-site associated DNA sequencing technology (RAD-seq) to evaluate a population of BC1F5 backcross lines (YVB × V20B); the RAD-seq data were used to construct a genetic linkage map with high-density SNPs for use in association analysis exploring genotype-phenotype relationships at the whole-genome level. A total of 17 quantitative trait loci (QTLs) for rice quality traits were mapped to chromosomes 3, 5, 6, 8, and 9. 8 major QTLs controlling different phenotypic variations were mapped to the same region of chromosome 5. This region contained the GS5 gene for grain weight and the qSW5/GW5 gene for grain width. This study provides new resources and insights into the molecular mechanisms of grain trait phenotypic variation and the transmission of genetic information via the introduction of genomic DNA to a distantly related crop relative species.

Identification of candidate genes for gelatinization temperature, gel consistency and pericarp color by GWAS in rice based on SLAF-sequencing

“…Gel consistency is inversely related to amylose content, we performed Pearson correlation analysis for gel consistency and amylose content trait, and reached the same conclusion (S5 Table). Many researchers believed that the Wx gene located on the Chromosome 6 of rice is the major gene controlling the gel consistency [44–46], and some other GC-related QTLs located on chromosome 1, 2, 3, 6, and 7 were also detected [47,48]. In 2014, in the whole panel and indica subpanel, GWAS detected a total of 28 and 24 significantly associated SNPs respectively, the QTL located in the interval of 1607061 bp-1958767 bp of chromosome 6, and the most significant associated SNP were both Chr6_1797551 (P=1.03x10E-17; P=3.62x10E-16) for both whole and indica panels (Fig 5, S6 Table).…”

Rice grain nutritional traits and their enhancement using relevant genes and QTLs through advanced approaches

“…At present, trends in molecular biology are fully updated. Therefore, by availing the different molecular approaches as, whole genome sequencing of 3000 rice accessions (Li et al 2014), Genome-wide association mapping (Huang et al 2010; Zhao et al 2011; Varshney et al 2014; McCouch et al 2016; Yano et al 2016; Wang et al 2016; Edzesi et al 2016; Biscarini et al 2016; Si et al 2016); Whole Genome SNP Array (Hu et al 2013; Yu et al 2014; Singh et al 2015; Malik et al 2016), Genomic-based genotyping platforms and re-sequencing (Gao et al 2013; Han and Huang 2013; Chen et al 2013; Barabaschi et al 2016; Guo et al 2014; Xu and Bai 2015), Genome-guided RNA-seq (Loraine et al 2013; Szczesniak et al 2013; Biselli et al 2015; Peng et al 2016; Badoni et al 2016), Map-based cloning approach (Salvi and Tuberosa 2005; Price 2006; Shomura et al 2008; Zhang et al 2013), Transcriptome profiling (Mochida and Shinozaki 2010; Chandel et al 2011; Venu et al 2011), Genomics approaches (Mochida and Shinozaki 2010; Swamy and Kumar 2013; Varshney et al 2014; Spindel et al 2015; Okazaki and Saito 2016) Sequencing-By-Synthesis (SBS) (Venu et al 2011; Sun et al 2015), Next generation sequencing (NGS) technologies (Uchida et al 2011; Miyao et al 2012; James et al 2013; Guo et al 2014; Wang et al 2016; Matsumoto et al 2016) and etc. could be strategically exploited to understand molecular mechanism and their relation between the genotypes and phenotypic traits.…”

“…Peng et al (2016) developed a stable variant line (YVB) having greatly improved grain quality traits using restriction-site associated DNA sequencing technology (RADseq) from a BC 1 F 5 backcross population derived from an indica hybrid rice maintainer line V20B and YVB line. The YVB is a stable variant line derived from V20B by transferring the genomic DNA of O. minuta into V20B using SIM method (Zhao et al 2005).…”

“…By availing the different molecular approaches and advanced genomic technologies such as SNPs array, genome sequencing, genome-wide association mapping, transcriptome profiling, etc. could be strategically exploited to understand molecular mechanism and their relation between the genotypes and phenotypic traits leading to development of improved rice varieties (Chandel et al 2011; Varshney et al 2014; Malik et al 2016; McCouch et al 2016; Peng et al 2016). …”

Insight into MAS: A Molecular Tool for Development of Stress Resistant and Quality of Rice through Gene Stacking

“…By exploring the diverse molecular techniques and advanced genomic technologies such as genome sequencing, SNPs array, genome-wide association mapping, and transcriptome profiling, the molecular mechanism and their relation between the genotypes and phenotypic traits leading to development of improved rice varieties can be realized (McCouch et al, 2016; Peng et al, 2016). Currently SSRs (second-generation markers) are widely used markers in MAS due to the easy availability and comparatively cheaper than others and they require a comparatively simple technique with a higher polymorphism rate (Gao et al, 2016).…”