Genome-wide association study of important agronomic traits within a core collection of rice (Oryza sativa L.)

Abstract

Background Cultivated rice ( Oryza sativa L.) is one of the staple food for over half of the world’s population. Thus, improvement of cultivated rice is important for the development of the world. It has been shown that abundant elite genes exist in rice landraces in previous studies. Results A genome-wide association study (GWAS) performed with EMMAX for 12 agronomic traits measured in both Guangzhou and Hangzhou was carried out using 150 accessions of Ting’s core collection selected based on 48 phenotypic traits from 2262 accessions of Ting’s collection, the GWAS included more than 3.8 million SNPs. Within Ting’s core collection, which has a simple population structure, low relatedness, and rapid linkage disequilibrium (LD) decay, we found 32 peaks located closely to previously cloned genes such as Hd1 , SD1 , Ghd7 , GW8 , and GL7 or mapped QTL, and these loci might be natural variations in the cloned genes or QTL which influence potentially agronomic traits. Furthermore, we also detected 32 regions where new genes might be located, and some peaks of these new candidate genes such as the signal on chromosome 11 for heading days were even higher than that of Hd1 . Detailed annotation of these significant loci were shown in this study. Moreover, according to the estimated LD decay distance of 100 to 350 kb on the 12 chromosomes in this study, we found 13 identical significant regions in the two locations. Conclusions This research provided important information for further mining these elite genes within Ting’s core collection and using them for rice breeding. Electronic supplementary material The online version of this article (10.1186/s12870-019-1842-7) contains supplementary material, which is available to authorized users.

Mining candidate gene for rice aluminum tolerance through genome wide association study and transcriptomic analysis

“…General linear model (GLM, without Q-matrix) and mixed linear model (MLM, K + Q) were performed using TASSEL software (www.maizegenetics.net/tassel). P ≤ 2.63 × 10 − 7 ( P = 1/n; n = total markers, which is a rough Bonferroni correction corresponding to -log 10 ( P ) = 6.58) should be defined as the suggestive threshold which is same to that in our previous study [52] in present study, but significant locus can not be identified according to this threshold. Thus, another significance threshold was calculated, i.e., a minimum Bayes factor (mBF).…”

“…After filtering the SNPs with low minor-allele frequency (5%), a total of 3,808,730 SNPs was remained for GWAS in our study. Please read more details in our previous study [52].…”

“…Genetic analyses were performed following our previous study [52]. Principal component analysis (PCA), and LD decay analysis among Ting’s core collection were performed based on all SNPs.…”

Genome Wide Association Studies on 7 Yield-related Traits of 183 Rice Varieties in Bangladesh

“…The results helped them to dig into the narrow genetic pool of European temperate rice and to identify the most relevant genetic components contributing to a high yield of this germplasm. Zhang et al (2019) [7] performed a GWAS with EMMAX for 12 agronomic traits using Ting's core collection (7128 rice landraces from all over China and from some of the other main rice-cultivating countries collected by Ying Ting [8]). Yang et al (2019) [9] detected SNP loci and determined related genes affecting the rice grain shape which lead to high-yielding breeding of rice.…”

“…The presence of multiple candidate genes within such a short candidate interval suggest further investigation to explore the causality of genes may be beneficial, and subsequently may facilitate the identification of advantageous genetic variations. Ya-fang et al [7] discovered GS2 loci in chromosome 2 in close association with GW. Therefore, our studies have notable similarities as well as dissimilarities with prior studies.…”