Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice

Guan Li; Yichen Cheng; Man Yin; Jinyu Yang; Jiezheng Ying; Changlan Zhu

doi:10.7717/peerj.12504

Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice

PeerJ. 2021 Nov 29:9:e12504. doi: 10.7717/peerj.12504. eCollection 2021.

Authors

Guan Li^#^{1

2}, Yichen Cheng^#², Man Yin², Jinyu Yang², Jiezheng Ying², Changlan Zhu¹

Affiliations

¹ School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang, Jiangxi Province, China.
² China National Rice Research Institute, Hangzhou, Zhejiang Province, China.

^# Contributed equally.

Abstract

Background: The panicle is the most important organ in rice, and all the panicle-related traits are correlated with rice grain yield. Understanding the underlying genetic mechanisms controlling panicle development is very important for improving rice production.

Methods: Nine panicle-related traits including heading date, panicle length, number of primary branches, number of secondary branches, number of grains per panicle, number of panicles per plant, number of filled grains per plant, seed-setting rate, and grain yield per plant were investigated. To map the quantitative trait loci (QTLs) for the nine panicle-related traits, a PCR-based genetic map with 208 markers (including 121 simple sequence repeats and 87 InDels) and a high-density linkage map with 18,194 single nucleotide polymorphism (SNP) markers were both used.

Results: Using a recombinant inbred line population derived from an indica variety Huanghuazhan and a japonica line Jizi 1560, a total of 110 and 112 QTLs were detected for panicle-related traits by PCR-based genetic map and by high-density linkage map, respectively. Most of the QTLs were clustered on chromosomes 1, 2, 3, 6, and 7 while no QTLs were detected on chromosome 10. Almost all the QTLs with LOD values of more than 5.0 were repeatedly detected, indicating the accuracy of the two methods and the stability of the QTL effects. No genes for panicle-related traits have been previously reported in most of these regions. QTLs found in JD1006-JD1007 and RM1148-RM5556 with high LOD and additive values deserved further research. The results of this study are beneficial for marker-assisted breeding and provide research foundation for further fine-mapping and cloning of these QTLs for panicle-related traits.

Keywords: Grain; Panicle; Quantitative trait locus; Recombinant inbred line; Rice; Yield.

Grants and funding

This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 31860373 and 32072050), the Key R&D Projects in Jiangxi Province of China (Grant No. 20192ACB60009), the Chinese High-yielding Transgenic Program (Grant No. 2016ZX08001-004) and the Zhejiang Provincial Natural Science Foundation of China (Grant No. LQ21C130003). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.