High-resolution Detection of Quantitative Trait Loci for Seven Important Yield-related Traits in Wheat (Triticum Aestivum L.) Using a High-density SLAF-seq Genetic Map

Overview

Journal BMC Genom Data

Publisher Biomed Central

Specialty Genetics

Date 2022 May 13

PMID 35562674

Authors

Tao Li

Qiao Li

Jinhui Wang

Zhao Yang

Yanyan Tang

Yan Su

Juanyu Zhang

Xvebing Qiu

Xi Pu

Zhifen Pan

Haili Zhang

Junjun Liang

Zehou Liu

Jun Li

Wuyun Yan

Maoqun Yu

Hai Long

Yuming Wei

Guangbing Deng

Affiliations

Soon will be listed here.

Abstract

Background: Yield-related traits including thousand grain weight (TGW), grain number per spike (GNS), grain width (GW), grain length (GL), plant height (PH), spike length (SL), and spikelet number per spike (SNS) are greatly associated with grain yield of wheat (Triticum aestivum L.). To detect quantitative trait loci (QTL) associated with them, 193 recombinant inbred lines derived from two elite winter wheat varieties Chuanmai42 and Chuanmai39 were employed to perform QTL mapping in six/eight environments.

Results: A total of 30 QTLs on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 4A, 5A, 5B, 6A, 6D, 7A, 7B and 7D were identified. Among them, six major QTLs QTgw.cib-6A.1, QTgw.cib-6A.2, QGw.cib-6A, QGl.cib-3A, QGl.cib-6A, and QSl.cib-2D explaining 5.96-23.75% of the phenotypic variance were detected in multi-environments and showed strong and stable effects on corresponding traits. Three QTL clusters on chromosomes 2D and 6A containing 10 QTLs were also detected, which showed significant pleiotropic effects on multiple traits. Additionally, three Kompetitive Allele Specific PCR (KASP) markers linked with five of these major QTLs were developed. Candidate genes of QTgw.cib-6A.1/QGl.cib-6A and QGl.cib-3A were analyzed based on the spatiotemporal expression patterns, gene annotation, and orthologous search.

Conclusions: Six major QTLs for TGW, GL, GW and SL were detected. Three KASP markers linked with five of these major QTLs were developed. These QTLs and KASP markers will be useful for elucidating the genetic architecture of grain yield and developing new wheat varieties with high and stable yield in wheat.

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References

McCartney C, Somers D, Humphreys D, Lukow O, Ames N, Noll J . Mapping quantitative trait loci controlling agronomic traits in the spring wheat cross RL4452x'AC Domain'. Genome. 2006; 48(5):870-83. DOI: 10.1139/g05-055. View

Su Q, Zhang X, Zhang W, Zhang N, Song L, Liu L . QTL Detection for Kernel Size and Weight in Bread Wheat ( L.) Using a High-Density SNP and SSR-Based Linkage Map. Front Plant Sci. 2018; 9:1484. PMC: 6193082. DOI: 10.3389/fpls.2018.01484. View

Ren T, Fan T, Chen S, Li C, Chen Y, Ou X . Utilization of a Wheat55K SNP array-derived high-density genetic map for high-resolution mapping of quantitative trait loci for important kernel-related traits in common wheat. Theor Appl Genet. 2021; 134(3):807-821. DOI: 10.1007/s00122-020-03732-8. View

Maccaferri M, Ricci A, Salvi S, Milner S, Noli E, Martelli P . A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. Plant Biotechnol J. 2014; 13(5):648-63. DOI: 10.1111/pbi.12288. View

Liu K, Sun X, Ning T, Duan X, Wang Q, Liu T . Genetic dissection of wheat panicle traits using linkage analysis and a genome-wide association study. Theor Appl Genet. 2018; 131(5):1073-1090. DOI: 10.1007/s00122-018-3059-9. View

Borrill P, Ramirez-Gonzalez R, Uauy C . expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform. Plant Physiol. 2016; 170(4):2172-86. PMC: 4825114. DOI: 10.1104/pp.15.01667. View

Miao J, Yang Z, Zhang D, Wang Y, Xu M, Zhou L . Mutation of RGG2, which encodes a type B heterotrimeric G protein γ subunit, increases grain size and yield production in rice. Plant Biotechnol J. 2018; 17(3):650-664. PMC: 6381795. DOI: 10.1111/pbi.13005. View

Dobrovolskaya O, Pont C, Sibout R, Martinek P, Badaeva E, Murat F . FRIZZY PANICLE drives supernumerary spikelets in bread wheat. Plant Physiol. 2014; 167(1):189-99. PMC: 4281007. DOI: 10.1104/pp.114.250043. View

Cao P, Liang X, Zhao H, Feng B, Xu E, Wang L . Identification of the quantitative trait loci controlling spike-related traits in hexaploid wheat (Triticum aestivum L.). Planta. 2019; 250(6):1967-1981. DOI: 10.1007/s00425-019-03278-0. View

10.

Tian X, Wen W, Xie L, Fu L, Xu D, Fu C . Molecular Mapping of Reduced Plant Height Gene in Bread Wheat. Front Plant Sci. 2017; 8:1379. PMC: 5550838. DOI: 10.3389/fpls.2017.01379. View

11.

Gao F, Wen W, Liu J, Rasheed A, Yin G, Xia X . Genome-Wide Linkage Mapping of QTL for Yield Components, Plant Height and Yield-Related Physiological Traits in the Chinese Wheat Cross Zhou 8425B/Chinese Spring. Front Plant Sci. 2016; 6:1099. PMC: 4683206. DOI: 10.3389/fpls.2015.01099. View

12.

Chai L, Chen Z, Bian R, Zhai H, Cheng X, Peng H . Correction to: Dissection of two quantitative trait loci with pleiotropic effects on plant height and spike length linked in coupling phase on the short arm of chromosome 2D of common wheat (Triticum aestivum L.). Theor Appl Genet. 2019; 132(11):3225. PMC: 6887850. DOI: 10.1007/s00122-019-03421-1. View

13.

Guan P, Lu L, Jia L, Kabir M, Zhang J, Lan T . Global QTL Analysis Identifies Genomic Regions on Chromosomes 4A and 4B Harboring Stable Loci for Yield-Related Traits Across Different Environments in Wheat ( L.). Front Plant Sci. 2018; 9:529. PMC: 5996883. DOI: 10.3389/fpls.2018.00529. View

14.

Chen Y, Yan Y, Wu T, Zhang G, Yin H, Chen W . Cloning of wheat keto-acyl thiolase 2B reveals a role of jasmonic acid in grain weight determination. Nat Commun. 2020; 11(1):6266. PMC: 7722888. DOI: 10.1038/s41467-020-20133-z. View

15.

Chen Y, Song W, Xie X, Wang Z, Guan P, Peng H . A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era. Mol Plant. 2020; 13(12):1694-1708. DOI: 10.1016/j.molp.2020.09.019. View

16.

Isham K, Wang R, Zhao W, Wheeler J, Klassen N, Akhunov E . QTL mapping for grain yield and three yield components in a population derived from two high-yielding spring wheat cultivars. Theor Appl Genet. 2021; 134(7):2079-2095. PMC: 8263538. DOI: 10.1007/s00122-021-03806-1. View

17.

Liu T, Wu L, Gan X, Chen W, Liu B, Fedak G . Mapping Quantitative Trait Loci for 1000-Grain Weight in a Double Haploid Population of Common Wheat. Int J Mol Sci. 2020; 21(11). PMC: 7311974. DOI: 10.3390/ijms21113960. View

18.

Yang J, Zhou Y, Wu Q, Chen Y, Zhang P, Zhang Y . Molecular characterization of a novel TaGL3-5A allele and its association with grain length in wheat (Triticum aestivum L.). Theor Appl Genet. 2019; 132(6):1799-1814. DOI: 10.1007/s00122-019-03316-1. View

19.

Yang W, Liu D, Li J, Zhang L, Wei H, Hu X . Synthetic hexaploid wheat and its utilization for wheat genetic improvement in China. J Genet Genomics. 2009; 36(9):539-46. DOI: 10.1016/S1673-8527(08)60145-9. View

20.

Cao S, Xu D, Hanif M, Xia X, He Z . Genetic architecture underpinning yield component traits in wheat. Theor Appl Genet. 2020; 133(6):1811-1823. DOI: 10.1007/s00122-020-03562-8. View