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Genomic confirmation of Gossypium barbadense introgression into G. hirsutum and a subsequent MAGIC population

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Abstract

Introgression of superior fiber traits from Pima cotton (Gossypium barbadense, GB) into high yield Upland cotton (G. hirsutum) has been a breeding objective for many years in a few breeding programs in the world. However, progress has been very slow due to introgression barriers resulting from whole genome hybridization between the two species. To minimize such barriers, chromosome substitution lines (CS-B) from Pima cotton 3–79 in an Upland cotton cultivar TM-1 were developed. A multiparent advanced generation inter-cross (MAGIC) population consisting of 180 recombinant inbred lines (RILs) was subsequently made using the 18 CS-B lines and three Upland cotton cultivars as parents. In this research, we sequenced the whole genomes of the 21 parents and 180 RILs to examine the G. barbadense introgression. Of the 18 CS-B lines, 11 contained the target GB chromosome or chromosome segment, two contained more than two GB chromosomes, and five did not have the expected introgression. Residual introgression in non-target chromosomes was prevalent in all CS-B lines. A clear structure existed in the MAGIC population and the 180 RILs were distributed into three groups, i.e., high, moderate, and low GB introgression. Large blocks of GB chromosome introgression were still present in some RILs after five cycles of random-mating, an indication of recombination suppression or other unknown reasons present in the population. Identity by descent analysis revealed that the MAGIC RILs contained less introgression than expected. This research presents an insight on understanding the complex problems of introgression between cotton species.

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Data availability

All relevant data reported in this paper are within the paper and its online supplementary files.

Abbreviations

CS-B:

Chromosome substitution from Gossypium barbadense

CSL:

Chromosome substitution line

CSIL:

Chromosome segment introgression line

CSSL:

Chromosome segment substitution line

GB:

Gossypium barbadense

IBD:

Identity by descent

IBS:

Identity by state

QTL:

Quantitative trait locus

MAGIC:

Multiparent advanced generation inter-cross;

RIL:

Recombinant inbred line

SNP:

Single nucleotide polymorphism

SSR:

Simple sequence repeat

UPGMA:

Unweighted pair group method with arithmetic mean

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Acknowledgements

This research was funded by the USDA-Agricultural Research Service CRIS project # 6054-21000-018-00D, and Cotton Incorporated projects #18-192 and #19-916. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA which is an equal opportunity provider and employer.

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Authors and Affiliations

  1. Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, 70124, USA

    David D. Fang & Gregory N. Thyssen

  2. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China

    Maojun Wang

  3. Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, 39762, USA

    Johnie N. Jenkins & Jack C. McCarty

  4. Cotton Incorporated, Cary, NC, 27513, USA

    Don C. Jones

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  1. David D. Fang
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  2. Gregory N. Thyssen
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  3. Maojun Wang
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  4. Johnie N. Jenkins
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  5. Jack C. McCarty
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  6. Don C. Jones
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Contributions

DDF: conceptualization, investigation, funding, methodology, supervision, and manuscript writing and revision; GNT: sequence data curation and analysis, manuscript writing and editing; MJW: sequence data analysis, manuscript reviewing and editing, JNJ and JCM: creation of plant materials, manuscript writing and editing; DCJ: funding, and manuscript reviewing and editing.

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Correspondence to David D. Fang.

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Communicated by Bing Yang.

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Supplementary Information

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Supplementary file1 (XLSX 2313 KB)

438_2022_1974_MOESM2_ESM.tif

Supplementary file2 (TIF 813 KB) Fig. S1. Identity by descent as in Fig. 4 plus contributions of Gossypium hirsutum cultivars. Blue is TM-1, Orange is SG747, Green is FM966; Pink is PSC355, and Red is G. barbadense 3-79

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Fang, D.D., Thyssen, G.N., Wang, M. et al. Genomic confirmation of Gossypium barbadense introgression into G. hirsutum and a subsequent MAGIC population. Mol Genet Genomics 298, 143–152 (2023). https://doi.org/10.1007/s00438-022-01974-3

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  • DOI: https://doi.org/10.1007/s00438-022-01974-3

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