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

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 in...

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Autores principales:	Guan Li, Yichen Cheng, Man Yin, Jinyu Yang, Jiezheng Ying, Changlan Zhu
Formato:	article
Lenguaje:	EN
Publicado:	PeerJ Inc. 2021
Materias:	Rice Panicle Grain Yield Quantitative trait locus Recombinant inbred line Medicine R
Acceso en línea:	https://doaj.org/article/45a18a3f8cd0418a8630dae66326efa8
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spelling	oai:doaj.org-article:45a18a3f8cd0418a8630dae66326efa82021-12-01T15:05:12ZDetection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice10.7717/peerj.125042167-8359https://doaj.org/article/45a18a3f8cd0418a8630dae66326efa82021-11-01T00:00:00Zhttps://peerj.com/articles/12504.pdfhttps://peerj.com/articles/12504/https://doaj.org/toc/2167-8359Background 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.Guan LiYichen ChengMan YinJinyu YangJiezheng YingChanglan ZhuPeerJ Inc.articleRicePanicleGrainYieldQuantitative trait locusRecombinant inbred lineMedicineRENPeerJ, Vol 9, p e12504 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Rice Panicle Grain Yield Quantitative trait locus Recombinant inbred line Medicine R
spellingShingle	Rice Panicle Grain Yield Quantitative trait locus Recombinant inbred line Medicine R Guan Li Yichen Cheng Man Yin Jinyu Yang Jiezheng Ying Changlan Zhu Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice
description	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.
format	article
author	Guan Li Yichen Cheng Man Yin Jinyu Yang Jiezheng Ying Changlan Zhu
author_facet	Guan Li Yichen Cheng Man Yin Jinyu Yang Jiezheng Ying Changlan Zhu
author_sort	Guan Li
title	Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice
title_short	Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice
title_full	Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice
title_fullStr	Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice
title_full_unstemmed	Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice
title_sort	detection of qtls for panicle-related traits using an indica × japonica recombinant inbred line population in rice
publisher	PeerJ Inc.
publishDate	2021
url	https://doaj.org/article/45a18a3f8cd0418a8630dae66326efa8
work_keys_str_mv	AT guanli detectionofqtlsforpaniclerelatedtraitsusinganindicajaponicarecombinantinbredlinepopulationinrice AT yichencheng detectionofqtlsforpaniclerelatedtraitsusinganindicajaponicarecombinantinbredlinepopulationinrice AT manyin detectionofqtlsforpaniclerelatedtraitsusinganindicajaponicarecombinantinbredlinepopulationinrice AT jinyuyang detectionofqtlsforpaniclerelatedtraitsusinganindicajaponicarecombinantinbredlinepopulationinrice AT jiezhengying detectionofqtlsforpaniclerelatedtraitsusinganindicajaponicarecombinantinbredlinepopulationinrice AT changlanzhu detectionofqtlsforpaniclerelatedtraitsusinganindicajaponicarecombinantinbredlinepopulationinrice
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Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice

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