Abstract
Rice is an important cereal in the world. The study of the genetic basis of important agronomic traits in rice landraces and identification of genes will facilitate the breed improvement. Gelatinization temperature (GT), gel consistency (GC) and pericarp color (PC) 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 GT, GC and PC, a total of 419 rice landraces core germplasm collections consisting of 330 indica lines, 78 japonica lines and 11 uncertain varieties were planted, collected, then GT, GC, PC were measured for two years, and sequenced using specific-locus amplified fragment sequencing (SLAF-seq) 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. 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.
Highlights
Rice is one of the most important food crops in the world [1].With the increasing standard of living of the people in China, the cooking and eating, and nutritional quality has attracted more attention
Many researches have reported the genetic basis of Gelatinization temperature (GT), gel consistency (GC) and pericarp color (PC)
Huang et al [12] detected 37 single nucleotide polymorphisms (SNPs) significantly associated with 14 agronomic traits by Genome-wide association study (GWAS) with 517 Chinese rice landraces, which per locus explained 36% of the phenotypic variation on average and 7 loci were consistent with the results of previous studies
Summary
Rice is one of the most important food crops in the world [1].With the increasing standard of living of the people in China, the cooking and eating, and nutritional quality has attracted more attention. GT and GC are important factors affecting cooking and eating quality of rice. Many researches have reported the genetic basis of GT, GC and PC. GC is an eating and cooking quality related trait with complicated genetic basis, and more than 20 QTLs for GC have been detected (http://www.gramene.org/) in rice, which located on chromosome 1, 2, 4, 6, 7, 11. Anthocyanin or proanthocyanidin biosynthesis pathway is a very complex process in plant [8], and molecular mechanism of pericarp anthocyanin and proanthocyanidin biosynthesis in rice is still unclear [9]
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