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Construction of genetic linkage map and genome dissection of domestication-related traits of moth bean (Vigna aconitifolia), a legume crop of arid areas

  • Chutintorn Yundaeng
  • Prakit SomtaEmail author
  • Kitiya Amkul
  • Alisa Kongjaimun
  • Akito Kaga
  • Norihiko TomookaEmail author
Original Article
  • 73 Downloads

Abstract

The moth bean (Vigna aconitifolia), possibly the most primitive crop of the genus Vigna, is a highly drought- and heat-resistant legume grown in arid areas. Moth bean domestication involved phenotypic changes, including reduction of seed dormancy and pod shattering, increased organ size, and earlier flowering and maturity. However, the genetics of the domestication process in moth bean is not known. In this study, we constructed a genetic linkage map for moth bean and used the map to identify quantitative trait loci (QTL) for domestication-related traits of an F2 population of 188 individuals produced from a cross of wild moth bean (TN67) and cultivated moth bean (ICPMO056). The genetic linkage map comprised 11 linkage groups (LG) of 172 simple sequence repeat markers and spanned a total length of 1016.8 centiMorgan (cM), with an average marker distance of 7.34 cM. A comparative genome analysis showed high genome synteny between moth bean and mungbean (Vigna radiata), adzuki bean (Vigna angularis), rice bean (Vigna umbellata), and yardlong bean (Vigna unguiculata). In total, 50 QTLs and 3 genes associated with 20 domestication-related traits were identified. Most of the QTLs belonged to five LGs (1, 2, 4, 7, and 10). Key traits related to domestication such as seed dormancy and pod shattering were controlled by large-effect QTLs (PVE > 20%) with one or two minor QTLs, whereas all other traits were controlled by one–seven minor QTLs, apart from seed weight, which was controlled by one major and seven minor QTLs. These results suggest that a small number of mutations with large phenotypic effects have contributed to the domestication of the moth bean. Comparative analysis of QTLs with related Vigna crops revealed that there are several domestication-related large-effect QTLs that had not been used in moth bean domestication. This study provides a basic genetic map and identified genome regions associated with domestication-related traits, which will be useful for the genetic improvement of the moth bean and related Vigna species.

Keywords

Domestication syndrome Moth bean Vigna aconitifolia Pod shattering Seed dormancy 

Notes

Acknowledgements

This research was supported by the Royal Golden Jubilee Ph.D. Program, the Thailand Research Fund. We are thankful to Chai Nat Field Crops Research Center, Thailand for field experiment in Thailand.

Funding

This research was supported by the Royal Golden Jubilee Ph.D. Program, the Thailand Research Fund.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethics approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Informed consent

Additional informed consent was obtained from all individual participants for whom identifying information is included in this article.

Supplementary material

438_2019_1536_MOESM1_ESM.pdf (1.4 mb)
Supplementary Fig. S1 Frequency distribution of domestication-related traits in F2 population derived from a cross between wild moth bean accession “TN67” and cultivated moth bean accession “ICPMO056” (PDF 1433 KB)
438_2019_1536_MOESM2_ESM.pdf (948 kb)
Supplementary Fig. S2 Frequency distribution of domestication-related traits in F2:3 population derived from a cross between wild moth bean accession “TN67” and cultivated moth bean accession “ICPMO056” (PDF 948 KB)
438_2019_1536_MOESM3_ESM.docx (16 kb)
Supplementary Table S1 Percentage of amplifiable and polymorphic SSR markers from four Vigna species in wild moth bean accession “TN67” and cultivated moth bean accession “ICPMO056” (DOCX 15 KB)
438_2019_1536_MOESM4_ESM.docx (18 kb)
Supplementary Table S2 Correlation between domestication-related traits in the F2 population of the cross between wild moth bean (TN73) and cultivated moth bean (IPCMO056). The population was grown in Japan during summer to rainy season 2014 (DOCX 18 KB)
438_2019_1536_MOESM5_ESM.docx (17 kb)
Supplementary Table S3 Correlation between domestication-related traits in the F2:3 population of the cross between cultivated moth bean (IPCMO056) and wild moth bean (TN67). The population was grown in Thailand during summer to rainy season of 2015 (DOCX 16 KB)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Agronomy, Faculty of Agriculture at Kampaheng SaenKasetsart UniversityKamphaeng SaenThailand
  2. 2.Center for Agricultural Biotechnology (AG-BIO/PEDRO-CHE)Kasetsart UniversityKamphaeng SaenThailand
  3. 3.Center of Advanced Studies for Agriculture and Food (CASAF), Kasetsart University Institute for Advanced StudiesKasetsart University (NRU-KU)BangkokThailand
  4. 4.Faculty of Animal Sciences and Agricultural TechnologySilpakorn UniversityCha-AmThailand
  5. 5.Soybean and Field Crop Applied Genomics Research UnitNational Agriculture and Food Research OrganizationTsukubaJapan
  6. 6.Genetic Resources CenterNational Agriculture and Food Research OrganizationTsukubaJapan

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