Genetic Dissection of an Allotetraploid Interspecific CSSLs Guides Interspecific Genetics and Breeding in Cotton

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2020 Jun 27

PMID 32586283

Citations 12

Authors

De Zhu

Ximei Li

Zhiwei Wang

Chunyuan You

Xinhui Nie

Jie Sun

Xianlong Zhang

Dawei Zhang

Zhongxu Lin

Affiliations

Soon will be listed here.

Abstract

Background: The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization.

Results: In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC).

Conclusions: This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.

Citing Articles

Genetic Regulatory Perturbation of Gene Expression Impacted by Genomic Introgression in Fiber Development of Allotetraploid Cotton.

Chen X, Hu X, Li G, Grover C, You J, Wang R Adv Sci (Weinh). 2024; 11(40):e2401549.

PMID: 39196795 PMC: 11515910. DOI: 10.1002/advs.202401549.

Dissecting the Superior Drivers for the Simultaneous Improvement of Fiber Quality and Yield Under Drought Stress Via Genome-Wide Artificial Introgressions of Gossypium barbadense into Gossypium hirsutum.

Han B, Zhang W, Wang F, Yue P, Liu Z, Yue D Adv Sci (Weinh). 2024; 11(34):e2400445.

PMID: 38984458 PMC: 11425955. DOI: 10.1002/advs.202400445.

Integrated Transcriptomic and Proteomic Characterization of a Chromosome Segment Substitution Line Reveals the Regulatory Mechanism Controlling the Seed Weight in Soybean.

Wei S, Yu Z, Du F, Cao F, Yang M, Liu C Plants (Basel). 2024; 13(6).

PMID: 38592937 PMC: 10975824. DOI: 10.3390/plants13060908.

Hub Genes in Stable QTLs Orchestrate the Accumulation of Cottonseed Oil in Upland Cotton via Catalyzing Key Steps of Lipid-Related Pathways.

Alam B, Liu R, Gong J, Li J, Yan H, Ge Q Int J Mol Sci. 2023; 24(23).

PMID: 38068920 PMC: 10706765. DOI: 10.3390/ijms242316595.

Gossypium mustelinum genome and an introgression population enrich interspecific genetics and breeding in cotton.

Yang Y, You C, Wang N, Wu M, Le Y, Wang M Theor Appl Genet. 2023; 136(6):130.

PMID: 37199762 DOI: 10.1007/s00122-023-04379-x.

References

Zhao Y, Wang Y, Huang Y, Cui Y, Hua J . Gene network of oil accumulation reveals expression profiles in developing embryos and fatty acid composition in Upland cotton. J Plant Physiol. 2018; 228:101-112. DOI: 10.1016/j.jplph.2018.06.002. View

Xu J, Zhao Q, Du P, Xu C, Wang B, Feng Q . Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.). BMC Genomics. 2010; 11:656. PMC: 3091774. DOI: 10.1186/1471-2164-11-656. View

Thomson M, Singh N, Dwiyanti M, Wang D, Wright M, Perez F . Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications. Rice (N Y). 2017; 10(1):40. PMC: 5577349. DOI: 10.1186/s12284-017-0181-2. View

Andres R, Coneva V, Frank M, Tuttle J, Samayoa L, Han S . Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.). Proc Natl Acad Sci U S A. 2016; 114(1):E57-E66. PMC: 5224360. DOI: 10.1073/pnas.1613593114. View

Garbowicz K, Liu Z, Alseekh S, Tieman D, Taylor M, Kuhalskaya A . Quantitative Trait Loci Analysis Identifies a Prominent Gene Involved in the Production of Fatty Acid-Derived Flavor Volatiles in Tomato. Mol Plant. 2018; 11(9):1147-1165. DOI: 10.1016/j.molp.2018.06.003. View

Watanabe S, Shimizu T, Machita K, Tsubokura Y, Xia Z, Yamada T . Development of a high-density linkage map and chromosome segment substitution lines for Japanese soybean cultivar Enrei. DNA Res. 2017; 25(2):123-136. PMC: 5909467. DOI: 10.1093/dnares/dsx043. View

Ademe M, He S, Pan Z, Sun J, Wang Q, Qin H . Association mapping analysis of fiber yield and quality traits in Upland cotton (Gossypium hirsutum L.). Mol Genet Genomics. 2017; 292(6):1267-1280. DOI: 10.1007/s00438-017-1346-9. View

Paran I, Zamir D . Quantitative traits in plants: beyond the QTL. Trends Genet. 2003; 19(6):303-6. DOI: 10.1016/S0168-9525(03)00117-3. View

Wang M, Tu L, Yuan D, Zhu D, Shen C, Li J . Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nat Genet. 2018; 51(2):224-229. DOI: 10.1038/s41588-018-0282-x. View

10.

Zhao B, Cao J, Hu G, Chen Z, Wang L, Shangguan X . Core cis-element variation confers subgenome-biased expression of a transcription factor that functions in cotton fiber elongation. New Phytol. 2018; 218(3):1061-1075. PMC: 6079642. DOI: 10.1111/nph.15063. View

11.

Yu Y, Yuan D, Liang S, Li X, Wang X, Lin Z . Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between gossypium hirsutum and G. barbadense. BMC Genomics. 2011; 12:15. PMC: 3031231. DOI: 10.1186/1471-2164-12-15. View

12.

Yang Z, Qanmber G, Wang Z, Yang Z, Li F . Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement. Trends Plant Sci. 2020; 25(5):488-500. DOI: 10.1016/j.tplants.2019.12.011. View

13.

Fang L, Wang Q, Hu Y, Jia Y, Chen J, Liu B . Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits. Nat Genet. 2017; 49(7):1089-1098. DOI: 10.1038/ng.3887. View

14.

Wan X, Wan J, Weng J, Jiang L, Bi J, Wang C . Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environments. Theor Appl Genet. 2005; 110(7):1334-46. DOI: 10.1007/s00122-005-1976-x. View

15.

Marillia E, Micallef B, Micallef M, Weninger A, Pedersen K, Zou J . Biochemical and physiological studies of Arabidopsis thaliana transgenic lines with repressed expression of the mitochondrial pyruvate dehydrogenase kinase. J Exp Bot. 2002; 54(381):259-70. DOI: 10.1093/jxb/erg020. View

16.

Wang J, Wan X, Crossa J, Crouch J, Weng J, Zhai H . QTL mapping of grain length in rice (Oryza sativa L.) using chromosome segment substitution lines. Genet Res. 2006; 88(2):93-104. DOI: 10.1017/S0016672306008408. View

17.

Balakrishnan D, Surapaneni M, Mesapogu S, Neelamraju S . Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. Theor Appl Genet. 2018; 132(1):1-25. DOI: 10.1007/s00122-018-3219-y. View

18.

Grover C, Gallagher J, Jareczek J, Page J, Udall J, Gore M . Re-evaluating the phylogeny of allopolyploid Gossypium L. Mol Phylogenet Evol. 2015; 92:45-52. DOI: 10.1016/j.ympev.2015.05.023. View

19.

Tyagi P, Gore M, Bowman D, Campbell B, Udall J, Kuraparthy V . Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.). Theor Appl Genet. 2013; 127(2):283-95. DOI: 10.1007/s00122-013-2217-3. View

20.

Qi L, Sun Y, Li J, Su L, Zheng X, Wang X . Identify QTLs for grain size and weight in common wild rice using chromosome segment substitution lines across six environments. Breed Sci. 2018; 67(5):472-482. PMC: 5790038. DOI: 10.1270/jsbbs.16082. View