Regional Association Analysis-based Fine Mapping of Three Clustered QTL for Verticillium Wilt Resistance in Cotton (G. Hirsutum. L)

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2017 Aug 27

PMID 28841857

Citations 6

Authors

Yunlei Zhao

Hongmei Wang

Wei Chen

Pei Zhao

Haiyan Gong

Xiaohui Sang

Yanli Cui

Affiliations

Soon will be listed here.

Abstract

Background: Verticillium wilt is one of the most destructive diseases affecting global cotton production. The most effective way to control wilt disease has been the development of new cotton varieties that are resistant to VW. VW-resistant Upland cotton cultivars have been created in both the USA and China by Gossypium barbadense introgression. More than 100 VW resistance quantitative trait loci have been detected.

Results: Three clustered VW resistance-related QTL were detected in a 120-line association population and assigned to a genome region of 14,653,469-55,190,112 bp in Dt_chr9. A regional association analysis-based fine-mapping strategy was developed to narrow down the confidence intervals of the above QTL. The estimated LD decay of the genome region of interest was much faster than those of the Dt_chr9 chromosome and the whole genome, suggesting the existence of a recombination hotspot. Thirty-seven haplotype blocks were detected. The confidence intervals of the three clustered QTL were narrowed down to a region of 937,906 bp involving QTL-i23734Gh and a region of 1,389,417 bp involving QTL- i10740Gh, respectively. Each region contained the strongest association signal. Comparative analysis redefined the confidence intervals of the other three QTLs, qDL52T2-c19, QTL-BNL4069, and QTL-JESPR0001. The broad-spectrum VW resistance QTL qVW-D9-1 was demonstrated to be closely linked with the three redefined QTL, QTL-i23734Gh, QTL- i10740Gh and QTL-JESPR0001. Twelve functional genes were detected to be located within the redefined confidence intervals of VW resistance QTL. The mRNA CotAD_60243, encoding E3 ubiquitin-protein ligase UPL2-like, responsible for plant innate immunity and broad-spectrum disease resistance, was found to be overlapped with the strongest association signal i10740Gh. Six mRNAs encoding putative disease-resistance proteins were within the redefined confidence interval of QTL-JESPR0001, suggesting a tandem arrangement of R genes.

Conclusions: Our results proved that the VW resistance effect related to three clustered VW resistance-related QTL was actually controled by two redefined major QTL and severlal minor loci. The broad-spectrum VW resistance QTL qVW-D9-1 may be closely linked with the two redefined major QTLs. The tandem arrangement of R genes were detected in the redefined confidence interval of QTL-JESPR0001. The candidate genes obtained should be helpful in identifying and characterizing defense genes related to VW resistance QTL.

Citing Articles

The Past, Present, and Future of Host Plant Resistance in Cotton: An Australian Perspective.

Egan L, Stiller W Front Plant Sci. 2022; 13:895877.

PMID: 35873986 PMC: 9297922. DOI: 10.3389/fpls.2022.895877.

Genome-Wide Identification of the Thaumatin-like Protein Family Genes in and Analysis of Their Responses to Infection.

Zhang Y, Chen W, Sang X, Wang T, Gong H, Zhao Y Plants (Basel). 2021; 10(12).

PMID: 34961118 PMC: 8708996. DOI: 10.3390/plants10122647.

Rapid Mining of Candidate Genes for Verticillium Wilt Resistance in Cotton Based on BSA-Seq Analysis.

Cui Y, Ge Q, Zhao P, Chen W, Sang X, Zhao Y Front Plant Sci. 2021; 12:703011.

PMID: 34691091 PMC: 8531640. DOI: 10.3389/fpls.2021.703011.

Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum.

Xu P, Guo Q, Meng S, Zhang X, Xu Z, Guo W BMC Genomics. 2021; 22(1):26.

PMID: 33407102 PMC: 7789578. DOI: 10.1186/s12864-020-07321-3.

Improvement of Wilt Resistance by Applying Arbuscular Mycorrhizal Fungi to a Cotton Variety with High Symbiotic Efficiency under Field Conditions.

Zhang Q, Gao X, Ren Y, Ding X, Qiu J, Li N Int J Mol Sci. 2018; 19(1).

PMID: 29342876 PMC: 5796189. DOI: 10.3390/ijms19010241.

References

Pritchard J, Stephens M, Donnelly P . Inference of population structure using multilocus genotype data. Genetics. 2000; 155(2):945-59. PMC: 1461096. DOI: 10.1093/genetics/155.2.945. View

Barrett J, Fry B, Maller J, Daly M . Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2004; 21(2):263-5. DOI: 10.1093/bioinformatics/bth457. View

Evanno G, Regnaut S, Goudet J . Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005; 14(8):2611-20. DOI: 10.1111/j.1365-294X.2005.02553.x. View

Konishi M, Sugiyama M . A novel plant-specific family gene, ROOT PRIMORDIUM DEFECTIVE 1, is required for the maintenance of active cell proliferation. Plant Physiol. 2006; 140(2):591-602. PMC: 1361326. DOI: 10.1104/pp.105.074724. View

Bradbury P, Zhang Z, Kroon D, Casstevens T, Ramdoss Y, Buckler E . TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007; 23(19):2633-5. DOI: 10.1093/bioinformatics/btm308. View

Wang H, Lin Z, Zhang X, Chen W, Guo X, Nie Y . Mapping and quantitative trait loci analysis of verticillium wilt resistance genes in cotton. J Integr Plant Biol. 2008; 50(2):174-82. DOI: 10.1111/j.1744-7909.2007.00612.x. View

Abdurakhmonov I, Kohel R, Yu J, Pepper A, Abdullaev A, Kushanov F . Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm. Genomics. 2008; 92(6):478-87. DOI: 10.1016/j.ygeno.2008.07.013. View

Abdurakhmonov I, Saha S, Jenkins J, Buriev Z, Shermatov S, Scheffler B . Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica. 2008; 136(3):401-17. DOI: 10.1007/s10709-008-9337-8. View

Jiang F, Zhao J, Zhou L, Guo W, Zhang T . Molecular mapping of Verticillium wilt resistance QTL clustered on chromosomes D7 and D9 in upland cotton. Sci China C Life Sci. 2009; 52(9):872-84. DOI: 10.1007/s11427-009-0110-8. View

10.

Zhang Z, Ersoz E, Lai C, Todhunter R, Tiwari H, Gore M . Mixed linear model approach adapted for genome-wide association studies. Nat Genet. 2010; 42(4):355-60. PMC: 2931336. DOI: 10.1038/ng.546. View

11.

Zhang W, Jian G, Jiang T, Wang S, Qi F, Xu S . Cotton gene expression profiles in resistant Gossypium hirsutum cv. Zhongzhimian KV1 responding to Verticillium dahliae strain V991 infection. Mol Biol Rep. 2012; 39(10):9765-74. DOI: 10.1007/s11033-012-1842-2. View

12.

Li H, Peng Z, Yang X, Wang W, Fu J, Wang J . Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat Genet. 2012; 45(1):43-50. DOI: 10.1038/ng.2484. View

13.

Zhang T, Qian N, Zhu X, Chen H, Wang S, Mei H . Variations and transmission of QTL alleles for yield and fiber qualities in upland cotton cultivars developed in China. PLoS One. 2013; 8(2):e57220. PMC: 3584144. DOI: 10.1371/journal.pone.0057220. View

14.

Zhang Y, Wang X, Ding Z, Ma Q, Zhang G, Zhang S . Transcriptome profiling of Gossypium barbadense inoculated with Verticillium dahliae provides a resource for cotton improvement. BMC Genomics. 2013; 14:637. PMC: 3849602. DOI: 10.1186/1471-2164-14-637. View

15.

Sun Q, Jiang H, Zhu X, Wang W, He X, Shi Y . Analysis of sea-island cotton and upland cotton in response to Verticillium dahliae infection by RNA sequencing. BMC Genomics. 2013; 14:852. PMC: 3878982. DOI: 10.1186/1471-2164-14-852. View

16.

Li X, Han Y, Wei Y, Acharya A, Farmer A, Ho J . Development of an alfalfa SNP array and its use to evaluate patterns of population structure and linkage disequilibrium. PLoS One. 2014; 9(1):e84329. PMC: 3887001. DOI: 10.1371/journal.pone.0084329. View

17.

Zhao Y, Wang H, Chen W, Li Y . Genetic structure, linkage disequilibrium and association mapping of Verticillium wilt resistance in elite cotton (Gossypium hirsutum L.) germplasm population. PLoS One. 2014; 9(1):e86308. PMC: 3900507. DOI: 10.1371/journal.pone.0086308. View

18.

Zhang X, Yuan Y, Wei Z, Guo X, Guo Y, Zhang S . Molecular mapping and validation of a major QTL conferring resistance to a defoliating isolate of verticillium wilt in cotton (Gossypium hirsutum L.). PLoS One. 2014; 9(4):e96226. PMC: 4004561. DOI: 10.1371/journal.pone.0096226. View

19.

Li F, Fan G, Wang K, Sun F, Yuan Y, Song G . Genome sequence of the cultivated cotton Gossypium arboreum. Nat Genet. 2014; 46(6):567-72. DOI: 10.1038/ng.2987. View

20.

Zhang T, Hu Y, Jiang W, Fang L, Guan X, Chen J . Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol. 2015; 33(5):531-7. DOI: 10.1038/nbt.3207. View