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

Abstract

Rice is an important cereal in the world, uncovering the genetic basis of agronomic traits in rice landraces genes associated with agronomically important traits is indispensable for both understanding the genetic basis of phenotypic variation and efficient crop improvement. Gelatinization temperature, gel consistency and pericarp color are important indices of rice cooking and eating quality evaluation and potential nutritional importance, which attract wide attentions in the application of genetic and breeding. To dissect the genetic basis of gelatinization temperature (GT), gel consistency (GC) and pericarp color (PC), a total of 419 rice landraces core germplasm collections consisting of 330 indica lines, 78 japonica lines and 11 uncertain varieties were grown, collected, then GT, GC, PC were measured for two years, and sequenced using Specific Locus Amplified Fragment Sequencing (SLAF) technology. In this study, 261,385,070 clean reads and 56,768 polymorphic SLAF tags were obtained, which a total of 211,818 single nucleotide polymorphisms (SNPs) were discovered. With 208,993 SNPs meeting the criterion of minor allele frequency (MAF) > 0.05 and integrity> 0.5, the phylogenetic tree and population structure analysis were performed for all 419 rice landraces, and the whole panel mainly separated into six subpopulations based on population structure analysis. Genome-wide association study (GWAS) was carried out for the whole panel, indica subpanel and japonica subpanel with subset SNPs respectively. One quantitative trait locus (QTL) on chromosome 6 for GT was detected in the whole panel and indica subpanel, and one QTL associated with GC was located on chromosome 6 in the whole panel and indica subpanel. For the PC trait, 8 QTLs were detected in the whole panel on chromosome 1, 3, 4, 7, 8, 10 and 11, and 7 QTLs in the indica subpanel on chromosome 3, 4, 7, 8, 10 and 11. The loci on chromosome 3, 8, 10 and 11 have not been identified previously, and they may be the candidate genes of pericarp color. For the three traits, no QTL was detected in japonica subpanel probably because of the polymorphism repartition between the subpanel, or small population size of japonica subpanel. This paper provides new gene resources and insights into the molecular mechanisms of important agricultural trait of rice phenotypic variation and genetic improvement of rice quality variety breeding.

Pair-wise Comparison Analysis for Multiple Pool-seq: an efficient method identified anthocyanin biosynthesis genes in rice pericarp

“…The region of 17.22-21.02 Mb interval on chromosome 3 is consistent with that reported in previous studies (Yang et al, 2018). There were 4620 SNPs with △(SNP-index)>=0.67, including 69 homozygous variant sites with △(SNP-index)=1…”

“…Finally, we selected three candidate regions that are shared for the real candidate regions, and the candidate gene Kala4 was just located in this region (Oikawa et al, 2015). Likewise, the overlapping regions of candidate regions B1-B2, B2-B3, and B1-B3 on chromosome 3 were used and the candidate region was finally determined to be 17.22-20.86 Mb interval and 20.94-21.02 Mb, which are consistent with our previous study (Yang et al, 2018). The final interval 2.76-5.46 Mb interval on chromosome 12 is only 17.7% of the maximum candidate interval.…”

“…Using PCAMP technology, we successfully identified 10 candidate intervals related to anthocyanin synthesis in rice seed coat. Among the 10 candidate intervals, Rd (Furukawa et al, 2007), OsCHI (Hong et al, 2012;Druka et al, 2003), and Kala4 (Oikawa et al, 2015) have been cloned, and two regions overlapped with that identified by provious GWAS study (Yang et al, 2018). These results validated the reliability of the method.…”

“…In the combinations of three colored pools, 17.22-20.86 Mb and 20.94-21.02 Mb of chromosome 3 were identified, which indicated that there were at least two key genes related to anthocyanin synthesis. In the previous study, we used 419 Core Germplasms of rice landraces in Guangxi for GWAS and identified that this region was an important candidate region for anthocyanin synthesis genes in rice pericarpdy (Yang et al, 2018). The Rd was located at 1.19 Mb upstream of the candidate region.…”

“…Plant materials. DLMM (rank No: C133) is the core germplasm of rice landraces in Guangxi (Yang et al, 2018). Its pericarp is black and the anthocyanin content is high.…”