Genome‐wide expression quantitative trait locus studies facilitate isolation of causal genes controlling panicle structure

Abstract

SUMMARYThe morphology of rice (Oryza sativa L.) panicles is an important determinant of grain yield, and elucidation of the genetic control of panicle structure is very important for fulfilling the demand for high yield in breeding programs. In a quantitative trait locus (QTL) study using 82 backcross inbred lines (BILs) derived from Koshihikari and Habataki, 68 QTLs for 25 panicle morphological traits were identified. Gene expression profiling from inflorescence meristems of BILs was obtained. A combination of phenotypic QTL (pQTL) and expression QTL (eQTL) analysis revealed co‐localization between pQTLs and eQTLs, consistent with significant correlations between phenotypic traits and gene expression levels. By combining pQTL and eQTL data, two genes were identified as controlling panicle structure: OsMADS18 modulates the average length of the primary rachis and OsFTL1 has pleiotropic effects on the total number of secondary rachides, number of grains per panicle, plant height and the length of flag leaves. Phenotypes were confirmed in RNA interference knocked‐down plants and overexpressor lines. The combination of pQTL and eQTL analysis could facilitate identification of genes involved in rice panicle formation.

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

“…Besides, the yield is also correlated to plant height, panicle length, seed setting rate, etc [3]. Several genes have been reported regulating the grains per panicle in rice, including Gn1a [4], GNP1 [5], GAD1 [6], An-1 [7], OsCBL8 [8], OsDim1 [8], OsMADS18 [9], PAY1 [10], and SAPK2 [11]. Gibberellins (GAs) and cytokinins play antagonistic roles in modulating the activity of the reproductive meristem.…”

Plant Polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains

“…We also observed that many of the genes that underwent PTGS by suppressed sRNA-mediated targeting in rice were previously implicated in reproductive growth and development (Additional File 6). For instance, OsMADS18 (APETALA1 homolog in rice), a member involved in floral architecture establishment (Wang et al 2020a), a close homolog of fertility restorer (RF) (Os10t0497366), glycine rich interaction partner of RF5 (Os12t0632000) (Hu et al 2012) and pollen specific desiccation associated protein (Os11t0167800) were targeted for degradation in kd lines (Additional File 6). In addition, these genes had reduced mRNA expression in kd lines.…”

“…8D). For instance, OsMADS18 (APETALA1 homolog in rice), a member involved in floral architecture establishment (Wang et al, 2020a), a close homolog of fertility restorer (RF) (Os10t0497366), glycine rich interaction partner of RF5 (Os12t0632000) (Hu et al, 2012) and pollen specific desiccation associated protein (Os11t0167800) were targeted for degradation in kd lines (Supplemental Table 3). In addition, these genes had reduced mRNA expression in kd lines.…”

Expressed genes and their new alleles identification during fibre elongation reveal the genetic factors underlying improvements of fibre length in cotton

“…, 2014; Wang et al. , 2020a). Regarding structural genomics, QTL mapping is a common genetic approach to expound on the genetic variations of phenotypic differentiation in various organisms (Beche et al.…”

“…Numerous new alleles generated by intragenic recombination have been identified in several plant species including maize, and some have shown transgressive expression (Liu et al, 2018). Additionally, expression quantitative trait locus (eQTL) mapping has emerged as a potentially powerful new approach to investigate the link between gene expression variation and phenotype, and the genetic network of genes in specific tissues has been clarified in many organisms Liu et al, 2017;Pang et al, 2019;Vosa et al, 2021;Wang et al, 2014;Wang et al, 2020a). Regarding structural genomics, QTL mapping is a common genetic approach to expound on the genetic variations of phenotypic differentiation in various organisms (Beche et al, 2020;Gangurde et al, 2020;Gu et al, 2020;Li et al, 2016).…”