基于BAAFS 90K芯片的小麦整合连锁图谱构建及产量相关性状QTL定位分析

doi:10.1016/j.jia.2023.07.028

Journal of Integrative Agriculture ›› 2024, Vol. 23 ›› Issue (11): 3641-3656.DOI: 10.1016/j.jia.2023.07.028

基于BAAFS 90K芯片的小麦整合连锁图谱构建及产量相关性状QTL定位分析

收稿日期:2023-04-12 接受日期:2023-06-21 出版日期:2024-11-20 发布日期:2024-10-10

Consensus linkage map construction and QTL mapping for eight yield-related traits in wheat using BAAFS 90K SNP array

Lihua Liu^{1, 2, 3*}, Pingping Qu^{1, 2, 3*}, Yue Zhou^{1, 2, 3}, Hongbo Li^{1, 2, 3}, Yangna Liu^{1, 2, 3}, Mingming Zhang^{1, 2, 3}, Liping Zhang^{1, 2, 3}, Changping Zhao^{1, 2, 3#}, Shengquan Zhang^{1, 2, 3#}, Binshuang Pang^{1, 2, 3#}

¹Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
²The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
³Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Beijing 100097, China

Received:2023-04-12 Accepted:2023-06-21 Online:2024-11-20 Published:2024-10-10
About author:Lihua Liu, Tel: +86-10-51503767, E-mail: llh216@163.com; Pingping Qu, Tel: +86-10-51503966, E-mail: quping070222@163.com; #Correspondence Binshuang Pang, Tel: +86-10-51503966, E-mail: pangbinshuang1122@aliyun.com; Shengquan Zhang, Tel: +86-10-51503104, E-mail: zsq8200@126.com; Changping Zhao, Tel: +86-10-51503968, E-mail: cp_zhao@vip.sohu.com * These authors contributed equally to this study.
Supported by:
This work was funded by the Major Project of Agricultural Biological Breeding, China (2022ZD0401902) and the Science and Technology Innovation Project of Beijing Academy of Agriculture and Forestry Sciences, China (KJCX20230301 and KJCX20230307).

摘要/Abstract

摘要：

利用不同群体和环境鉴定产量相关稳定数量性状位点(QTL)对小麦育种和遗传学研究至关重要。整合连锁图谱在小麦遗传学和基因组学研究中发挥着重要作用。本研究利用2个小麦双亲群体（即京花1号×小白冬麦DH群体和L43×陕西白麦F₂群体）和小麦BAAFS 90K SNP 芯片构建了一张小麦整合连锁图谱。整合连锁图谱总长为5437.92厘摩，共包括44,503个SNP标记。整合图谱中标记的顺序与其在单群体连锁图谱和小麦参考基因组IWGSC RefSeq v2.1中的顺序均具有较高的共线性。分别在6个，2个和2个环境中采集了京花1号×小白冬麦DH群体和L43×陕西白麦衍生的F_2:3、F_2:4群体的8个产量相关性状进行QTL定位分析。采用完备区间作图法共定位到32个与产量相关的环境稳定QTL。其中，4个QTL，即QPH.baafs-4B，QKNS.baafs-4B，QTGW.baafs-4和QSL.baafs-5A.3，能在多个群体和环境中被重复检测到。7个稳定的QTL，即QPH.baafs-2B，QKNS.baafs-3D，QSL.baafs-3D，QKW.baafs-4B，QPH.baafs-5D，QPH.baafs-6A.1和QSL.baafs-6A，在前人的研究中没有被报道过。4B染色体上的17.25~44.91Mb与6个产量相关性状相关，是影响产量性状的重要区段。矮杆基因Rht24周围含有控制粒长、粒宽、穗长和千粒重的QTL，这些QTL可能来自Rht24的一因多效，也可能是与其紧密连锁的位点。本研究针对稳定QTL共鉴定到254个候选基因，其中TraesCS5A03G1264300，TraesCS1B03G0624000和TraesCS6A03G0697000值得特别关注，因为它们的同源基因已被证实能调控相应的性状。本研究构建的整合连锁图谱和鉴定到的稳定产量相关性状QTL及其候选基因将有益于小麦产量相关性状的遗传解析，并有助于加快培育兼具理想株型形态和高产的小麦新品种。

Abstract:

Identifying stable quantitative trait loci (QTLs) for yield-related traits across populations and environments is crucial for wheat breeding and genetic studies. Consensus maps also play important roles in wheat genetic and genomic research. In the present study, a wheat consensus map was constructed using a doubled haploid (DH) population derived from Jinghua 1×Xiaobaidongmai (JX), an F₂ population derived from L43×Shanxibaimai (LS) and the BAAFS Wheat 90K SNP array single nucleotide polymorphism (SNP) array. A total of 44,503 SNP markers were mapped on the constructed consensus map, and they covered 5,437.92 cM across 21 chromosomes. The consensus map showed high collinearity with the individual maps and the wheat reference genome IWGSC RefSeq v2.1. Phenotypic data on eight yield-related traits were collected in the JX population, as well as the F_2:3 and F_2:4 populations of LS, in six, two and two environments, respectively, and those data were used for QTL analysis. Inclusive composite interval mapping (ICIM) identified 32 environmentally stable QTLs for the eight yield-related traits. Among them, four QTLs (QPH.baafs-4B, QKNS.baafs-4B, QTGW.baafs-4B, and QSL.baafs-5A.3) were detected across mapping populations and environments, and nine stable QTLs (qKL.baafs-1D, QPH.baafs-2B, QKNS.baafs-3D, QSL.baafs-3D, QKW.baafs-4B, QPH.baafs-5D, QPH.baafs-6A.1, QSL.baafs-6A, and QSL.baafs-6D) are likely to be new. The physical region of 17.25–44.91 Mb on chromosome 4B was associated with six yield-related traits, so it is an important region for wheat yield. The physical region around the dwarfing gene Rht24 contained QTLs for kernel length (KL), kernel width (KW), spike length (SL), and thousand-grain weight (TGW), which are either from a pleiotropic effect of Rht24 or closely linked loci. For the stable QTLs, 254 promising candidate genes were identified. Among them, TraesCS5A03G1264300, TraesCS1B03G0624000 and TraesCS6A03G0697000 are particularly noteworthy since their homologous genes have similar functions for the corresponding traits. The constructed consensus map and the identified QTLs along with their candidate genes will facilitate the genetic dissection of wheat yield-related traits and accelerate the development of wheat cultivars with desirable plant morphology and high yield.

Key words: consensus map , QTL , yield-related traits , wheat (Triticum aestivum L.)

Lihua Liu, Pingping Qu, Yue Zhou, Hongbo Li, Yangna Liu, Mingming Zhang, Liping Zhang, Changping Zhao, Shengquan Zhang, Binshuang Pang. 基于BAAFS 90K芯片的小麦整合连锁图谱构建及产量相关性状QTL定位分析[J]. Journal of Integrative Agriculture, 2024, 23(11): 3641-3656.

Lihua Liu, Pingping Qu, Yue Zhou, Hongbo Li, Yangna Liu, Mingming Zhang, Liping Zhang, Changping Zhao, Shengquan Zhang, Binshuang Pang. Consensus linkage map construction and QTL mapping for eight yield-related traits in wheat using BAAFS 90K SNP array[J]. Journal of Integrative Agriculture, 2024, 23(11): 3641-3656.

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基于BAAFS 90K芯片的小麦整合连锁图谱构建及产量相关性状QTL定位分析

Consensus linkage map construction and QTL mapping for eight yield-related traits in wheat using BAAFS 90K SNP array

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