Identification, pyramid and candidate genes of QTLs for associated traits based on a dense erect panicle rice CSSL-Z749 and five SSSLs, three DSSLs and one TSSL

Dachuan Wang,Qiuli Zhang,Guanghua He,Fangming Zhao,Naz Farkhanda,Kai Zhou,Ruxiang Li,Yinghua Ling,Peixuan Liang,Siqian Xiang,Miaomiao Li

doi:10.1186/s12284-021-00496-7

Dachuan Wang, Qiuli Zhang + Show 9 more

Open Access

https://doi.org/10.1186/s12284-021-00496-7

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Journal: Rice	Publication Date: Jun 16, 2021
Citations: 5	License type: open-access

Affiliation: Southwest University, Rice Research Institute

Abstract

BackgroundSeed-set density is an important agronomic trait in rice. However, its genetic mechanism is complex. Chromosome segment substitution lines (CSSLs) are ideal materials for studying complex traits.ResultsA rice CSSL, Z749, with a dense and erect panicle phenotype, was identified among progeny of the recipient parent Nipponbare and the donor parent Xihui 18. Z749 carried seven substitution segments (average length 2.12 Mb). Compared with Nipponbare, Z749 showed significant increases in the numbers of primary (NPB) and secondary branches (NSB), number of spikelets (SPP) and grains per panicle (GPP), seed-set density (SSD), and decrease in panicle length (PL). A secondary F2 population derived from a cross between Nipponbare and Z749 was used to map quantitative trait loci (QTLs) for associated traits. Fifteen QTLs distributed on chromosomes 5, 7, 8, and 10 were detected. The QTL qPL7 might be an allele of OsFAD8 and the remaining 14 QTLs (e.g., qSSD5 and qSSD10 etc.) might be novel. Fourteen QTLs were verified using five single-segment substitution lines (SSSLs). The seed-set density of Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). The QTLs qSSD10, qSSD5, and qSSD8 were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, and 8, respectively. Analysis of QTL additive effects indicated that qSSD5, qSSD8, and qSSD10 from Xihui18 increased seed-set density of Z749 by 14.10, 11.38, and 5.11 spikelets per 10 cm panicle, respectively. Analysis of QTL epistatic effects revealed that pyramiding of qSSD5 and qSSD8, qSSD5 and qSSD10, qSSD8 and qSSD10, and qSSD5, qSSD8 and qSSD10 produced novel genotypes with increased seed-set density.ConclusionsInheritance of seed-set density in Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). Then, they were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, 8, respectively. Two MAPK genes (OsMPK9 and OsMPK17) and one gene (candidate gene 6) involved in auxin metabolism might be candidate genes for qSSD5, and OsSAUR32 might be the candidate gene for qSSD8. Pyramiding of qSSD5, qSSD8, and qSSD10 enhanced seed-set density.

Highlights

Seed-set density is an important agronomic trait in rice
Identification of substitution segments in Z749 Identification of the substitution segments and detection of the genetic background purity were performed on 10 individuals of the Z749 lines using all simple sequence repeat (SSR) markers located on the seven substitution segments of Z749 and 24 SSR markers, which were in turn located outside the substitution segments
Phenotypes of Chromosome segment substitution lines (CSSLs)-Z749 Compared with Nipponbare, CSSL-Z749 showed significant increase in number of grains per panicle, number of spikelets per panicle, number of primary branches, number of secondary branches, and seed-set density (Fig. 2A, B), which were increased by 15.51 %, 23.92 %, 29.57 %, 23.65 %, and 59.42 % (Fig. 2G, E, H, I, D), Fig. 1 Substitution segments and detected Quantitative trait locus (QTL) in Z749

Summary

Introduction

Seed-set density is an important agronomic trait in rice. Panicle architecture is an important agronomic trait that affects seed-set density and is strongly associated with grain yield. The genetic mechanism for seed-set density is complex and controlled by multiple genes. A number of genes have been shown to affect the architecture of the rice panicle Some of these genes are involved in the hormone signaling pathways of phytohormones, such as cytokinins, auxin, and brassinolactone. Genes associated with the auxin metabolism pathway include PAY1 (PLANT ARCHITECTURE AND YIEL D 1), LAX1 (LAX PANICLE 1), SPA (SMALL PANICLE), and ASP1 (ABERRANT SPIKELET AND PANICLE1). The cpb mutant shows phenotypes of increased BR-sensitivity, clustered primary branches of the panicle, and smaller seeds (Wu et al 2016) It remains unclear how brassinolide affects panicle development. It is necessary to identify additional genes that influence the dense panicle architecture of rice

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