Uncovering the genetic mechanisms regulating panicle architecture in rice with GPWAS and GWAS

Abstract

Background The number of panicles per plant, number of grains per panicle, and 1000-grain weight are important factors contributing to the grain yield per plant in rice. The Rice Diversity Panel 1 (RDP1) contains a total of 421 purified, homozygous rice accessions representing diverse genetic variations within O. sativa. The release of High-Density Rice Array (HDRA, 700 k SNPs) dataset provides a new opportunity to discover the genetic variants of panicle architectures in rice. Results In this report, a new method genome-phenome wide association study (GPWAS) was performed with 391 individuals and 27 traits derived from RDP1 to scan the relationship between the genes and multi-traits. A total of 1985 gene models were linked to phenomic variation with a p-value cutoff of 4.49E-18. Besides, 406 accessions derived from RDP1 with 411,066 SNPs were used to identify QTLs associated with the total spikelets number per panicle (TSNP), grain number per panicle (GNP), empty grain number per panicle (EGNP), primary branch number (PBN), panicle length (PL), and panicle number per plant (PN) by GLM, MLM, FarmCPU, and BLINK models for genome-wide association study (GWAS) analyses. A total of 18, 21, 18, 17, 15, and 17 QTLs were identified tightly linked with TSNP, GNP, EGNP, PBN, PL, and PN, respectively. Then, a total of 23 candidate genes were mapped simultaneously using both GWAS and GPWAS methods, composed of 6, 4, 5, 4, and 4 for TSNP, GNP, EGNP, PBN, and PL. Notably, one overlapped gene (Os01g0140100) were further investigated based on the haplotype and gene expression profile, indicating this gene might regulate the TSNP or panicle architecture in rice. Conclusions Nearly 30 % (30/106) QTLs co-located with the previous published genes or QTLs, indicating the power of GWAS. Besides, GPWAS is a new method to discover the relationship between genes and traits, especially the pleiotropy genes. Through comparing the results from GWAS and GPWAS, we identified 23 candidate genes related to panicle architectures in rice. This comprehensive study provides new insights into the genetic basis controlling panicle architectures in rice, which lays a foundation in rice improvement.

Prototype for developing SNP markers from GWAS and biparental QTL for rice panicle and grain traits

“…Also, there was an association between DB69 (chr. 8) and panicle length, supporting the GWAS-QTL reported by Zhong et al (2021).…”

“…11) targeted rice minicore GWAS-QTL(Huggins et al, 2019), but only DB6 had overlapping RIL-QTL. Of note, recentlyZhong et al (2021) reanalyzed T A B L E 1 Eighteen single nucleotide polymorphism (SNP) markers developed from significant SNPs identified in genomewide association studies quantitative trait loci (GWAS-QTL). Sixteen markers were colocated with Estrela × NSFTV199 recombinant inbred line (RIL) QTL.…”

Genetic Diversity Relationship Between Grain Quality and Appearance in Rice

“…The detailed information of samples used in this study was listed in Supplementary Table 1 . The same procedure was used to preprocess the genotype data set with a previous study (Zhong et al, 2021 ).…”

Molecular and Transcriptional Regulation of Seed Development in Cereals: Present Status and Future Prospects

“…To explore candidate genes underlying yield related traits, GWAS were conducted to identify underlying loci for each phenotype. Association mapping has been used to successfully discover significant marker-trait associations in cereal crops including rice [51][52][53][54] and wheat [55][56][57][58]. A large number of wellcharacterized QTLs such as GW2, GIF1, qSW5, GS3 and qGL7 in rice [59][60][61][62][63] and more than 40 QTL including TaGW2 [64][65][66] associated with kernel morphological traits such as kernel length, kernel width, kernel thickness, kernel length/width ratio, kernel length/thickness ratio, kernel width/thickness ratio, flag leaf width, length and area have been recently identified and mapped in wheat [67][68][69][70].…”