Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte

Abstract Background Teosinte ear bears single spikelet, whereas maize ear bears paired spikelets, doubling the number of grains in each cupulate during maize domestication. In the past 20 years, genetic analysis of single vs. paired spikelets (PEDS) has been stagnant. A better understanding of genet...

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Autores principales:	Zhengjie Chen, Dengguo Tang, Kun Hu, Lei Zhang, Yong Yin, Jixing Ni, Peng Li, Le Wang, Tingzhao Rong, Jian Liu
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Maize domestication Single vs. paired spikelets QTL-seq Major QTL Epistasis Photoperiod Botany QK1-989
Acceso en línea:	https://doaj.org/article/3238bdfe42474e30b443c34247605a66
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spelling	oai:doaj.org-article:3238bdfe42474e30b443c34247605a662021-12-05T12:06:24ZCombining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte10.1186/s12870-021-03353-31471-2229https://doaj.org/article/3238bdfe42474e30b443c34247605a662021-12-01T00:00:00Zhttps://doi.org/10.1186/s12870-021-03353-3https://doaj.org/toc/1471-2229Abstract Background Teosinte ear bears single spikelet, whereas maize ear bears paired spikelets, doubling the number of grains in each cupulate during maize domestication. In the past 20 years, genetic analysis of single vs. paired spikelets (PEDS) has been stagnant. A better understanding of genetic basis of PEDS could help fine mapping of quantitative trait loci (QTL) and cloning of genes. Results In this study, the advanced mapping populations (BC3F2 and BC4F2) of maize × teosinte were developed by phenotypic recurrent selection. Four genomic regions associated with PEDS were detected using QTL-seq, located on 194.64–299.52 Mb, 0–162.80 Mb, 12.82–97.17 Mb, and 125.06–157.01 Mb of chromosomes 1, 3, 6, and 8, respectively. Five QTL for PEDS were identified in the regions of QTL-seq using traditional QTL mapping. Each QTL explained 1.12–38.05% of the phenotypic variance (PVE); notably, QTL qPEDS3.1 with the average PVE of 35.29% was identified in all tests. Moreover, 14 epistatic QTL were detected, with the total PVE of 47.57–66.81% in each test. The QTL qPEDS3.1 overlapped with, or was close to, one locus of 7 epistatic QTL. Near-isogenic lines (NILs) of QTL qPEDS1.1, qPEDS3.1, qPEDS6.1, and qPEDS8.1 were constructed. All individuals of NIL-qPEDS6.1(MT1) and NIL-qPEDS8.1(MT1) showed paired spikelets (PEDS = 0), but the flowering time was 7 days shorter in the NIL-qPEDS8.1(MT1). The ratio of plants with PEDS > 0 was low (1/18 to 3/18) in the NIL-qPEDS1.1(MT1) and NIL-qPEDS3.1(MT1), maybe due to the epistatic effect. Conclusion Our results suggested that major QTL, minor QTL, epistasis and photoperiod were associated with the variation of PEDS, which help us better understand the genetic basis of PEDS and provide a genetic resource for fine mapping of QTL.Zhengjie ChenDengguo TangKun HuLei ZhangYong YinJixing NiPeng LiLe WangTingzhao RongJian LiuBMCarticleMaize domesticationSingle vs. paired spikeletsQTL-seqMajor QTLEpistasisPhotoperiodBotanyQK1-989ENBMC Plant Biology, Vol 21, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Maize domestication Single vs. paired spikelets QTL-seq Major QTL Epistasis Photoperiod Botany QK1-989
spellingShingle	Maize domestication Single vs. paired spikelets QTL-seq Major QTL Epistasis Photoperiod Botany QK1-989 Zhengjie Chen Dengguo Tang Kun Hu Lei Zhang Yong Yin Jixing Ni Peng Li Le Wang Tingzhao Rong Jian Liu Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte
description	Abstract Background Teosinte ear bears single spikelet, whereas maize ear bears paired spikelets, doubling the number of grains in each cupulate during maize domestication. In the past 20 years, genetic analysis of single vs. paired spikelets (PEDS) has been stagnant. A better understanding of genetic basis of PEDS could help fine mapping of quantitative trait loci (QTL) and cloning of genes. Results In this study, the advanced mapping populations (BC3F2 and BC4F2) of maize × teosinte were developed by phenotypic recurrent selection. Four genomic regions associated with PEDS were detected using QTL-seq, located on 194.64–299.52 Mb, 0–162.80 Mb, 12.82–97.17 Mb, and 125.06–157.01 Mb of chromosomes 1, 3, 6, and 8, respectively. Five QTL for PEDS were identified in the regions of QTL-seq using traditional QTL mapping. Each QTL explained 1.12–38.05% of the phenotypic variance (PVE); notably, QTL qPEDS3.1 with the average PVE of 35.29% was identified in all tests. Moreover, 14 epistatic QTL were detected, with the total PVE of 47.57–66.81% in each test. The QTL qPEDS3.1 overlapped with, or was close to, one locus of 7 epistatic QTL. Near-isogenic lines (NILs) of QTL qPEDS1.1, qPEDS3.1, qPEDS6.1, and qPEDS8.1 were constructed. All individuals of NIL-qPEDS6.1(MT1) and NIL-qPEDS8.1(MT1) showed paired spikelets (PEDS = 0), but the flowering time was 7 days shorter in the NIL-qPEDS8.1(MT1). The ratio of plants with PEDS > 0 was low (1/18 to 3/18) in the NIL-qPEDS1.1(MT1) and NIL-qPEDS3.1(MT1), maybe due to the epistatic effect. Conclusion Our results suggested that major QTL, minor QTL, epistasis and photoperiod were associated with the variation of PEDS, which help us better understand the genetic basis of PEDS and provide a genetic resource for fine mapping of QTL.
format	article
author	Zhengjie Chen Dengguo Tang Kun Hu Lei Zhang Yong Yin Jixing Ni Peng Li Le Wang Tingzhao Rong Jian Liu
author_facet	Zhengjie Chen Dengguo Tang Kun Hu Lei Zhang Yong Yin Jixing Ni Peng Li Le Wang Tingzhao Rong Jian Liu
author_sort	Zhengjie Chen
title	Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte
title_short	Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte
title_full	Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte
title_fullStr	Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte
title_full_unstemmed	Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte
title_sort	combining qtl-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte
publisher	BMC
publishDate	2021
url	https://doaj.org/article/3238bdfe42474e30b443c34247605a66
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Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte

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