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Evolutionary aspects of direct or indirect selection for seed size and seed metabolites in Brassica juncea and diploid progenitor species

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Abstract

Seed size and seed metabolites have been the targets of direct or indirect selection during domestication and subsequent crop breeding. Understanding these traits and associated genetics can prove very useful for plant translational research. Large germplasm assemblage (235) of Brassica juncea and its progenitor species (B. rapa and B. nigra) was evaluated to establish seed trait variations for seed size and seed metabolites. Seeds were smallest in B. nigra and largest in B. juncea. Australian B. juncea and Indian B. rapa var brown sarson types averaged more seed oil content. Seed size and oil content were generally higher in modern cultivars in comparison to the land races. Allelic diversity for known associated genes for seed-size and oil-content (AP2, ARF2, TTG2, GRF2, GL2, CYP78A5, CYP78A6, MINI3, IKU2, IKU1, BRI1, DGAT, GPDH, LPAAT, GPAT and DA1) was studied so as to infer the effect of domestication on seed traits. Three genes (IKU1, IKU2, AP2) in B. rapa, two (TTG2 and GL2) in B. nigra and two (IKU1 and GRF2) in natural B. juncea were identified as targets of selection on the basis of Fst outlier and/or sequence diversity tests. We report parallel divergence for seed traits between B. juncea and B. rapa. Directional selection appeared stronger for seed-size as compared to correlated seed metabolites. Positive selection on seed-size is likely to have played a significant role in structuring regional variation in the germplasm.

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Acknowledgements

The studies were financially supported by the Indian Council of Agricultural Research under ICAR National Professor Project “Broadening the genetic base of Indian mustard (Brassica juncea) through alien introgressions and germplasm enhancement” awarded to S.S.B. The authors thank “Plant Gene Resources of Canada, Agriculture and Agri-Food Canada” for providing many of the germplasm lines used in our studies.

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Authors and Affiliations

  1. Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India

    Meha Sharma, Gurpreet Kaur, Sanjula Sharma, Javed Akhatar, Anju Sharma & S. S. Banga

  2. School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India

    Simarjeet Kaur Sra

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Correspondence to S. S. Banga.

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Supplementary Tables (DOCX 41 KB)

11033_2019_4591_MOESM2_ESM.tiff

Decay of linkage disequilibrium (LD) in different subpopulations of B. rapa; A) rapCA for DA1, CYP78A6, CYP78A5, AP2, GRF2, MINI3, IKU2, IKU1, BRI1, DGAT, GPDH, LPAAT, GPAT and GL2 genes, B) rapCAN for DA1, TTG2, CYP78A6, CYP78A5, AP2, GRF2, MINI3, IKU2, IKU1, BRI1, DGAT, GPDH, LPAAT, GPAT and GL2 genes, C) rapIT for DA1, TTG2, CYP78A6, CYP78A5, AP2, GRF2, MINI3, IKU2, IKU1, BRI1, DGAT, GPDH, LPAAT, GPAT and GL2 genes, D) rapPB for DA1, CYP78A6, CYP78A5, AP2, GRF2, MINI3, IKU2, IKU1, BRI1, DGAT, GPDH, LPAAT, GPAT and GL2 genes and E) rapIB for DA1, TTG2, CYP78A6, AP2, GRF2, MINI3, IKU2, IKU1, BRI1, DGAT, GPDH, LPAAT, GPAT and GL2 genes—Supplementary Fig. 1 (TIFF 1520 KB)

11033_2019_4591_MOESM3_ESM.tiff

Decay of linkage disequilibrium (LD) in different subpopulations of B. nigra; A) nigCAN for DA1, ARF2, CYP78A6, CYP78A5, AP2, GRF2, MINI3, IKU2, IKU1, BRI1, DGAT, LPAAT, GPAT and GL2 genes and B) nigI for DA1, TTG2, CYP78A5, AP2, GRF2,MINI3, IKU2, IKU1, BRI1, DGAT, LPAAT, GPAT and GL2 genes—Supplementary Fig. 2 (TIFF 675 KB)

11033_2019_4591_MOESM4_ESM.tiff

Decay of linkage disequilibrium (LD) in different subpopulations of B. juncea; A) junA for DA1, TTG2, CYP78A6, CYP78A5, AP2, ARF2, GRF2, MINI3, IKU2, IKU1, BRI1, DGAT, GPDH, LPAAT, GPAT and GL2 genes, B) junC for DA1, TTG2, CYP78A5, AP2, GRF2, MINI3, IKU2, IKU1, BRI1, DGAT, GPDH, LPAAT, GPAT and GL2 genes, C) junEE for DA1, TTG2, CYP78A6, CYP78A5, AP2, GRF2, MINI3, IKU2, IKU1, BRI1, DGAT, GPDH, LPAAT, GPAT and GL2 genes and D) junI for DA1, TTG2, CYP78A6, CYP78A5, AP2, GRF2, MINI3, IKU2, IKU1, BRI1, DGAT, GPDH, LPAAT, GPAT and GL2 genes—Supplementary Fig. 3 (TIFF 1334 KB)

11033_2019_4591_MOESM5_ESM.tiff

Candidate loci under directional and balancing selection identified using Bayescan, Arlequin and LOSITAN softwares in B. rapa (A–C), B. nigra (D–F) and B. juncea (G–I)—Supplementary Fig. 4 (TIFF 327 KB)

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Sra, S.K., Sharma, M., Kaur, G. et al. Evolutionary aspects of direct or indirect selection for seed size and seed metabolites in Brassica juncea and diploid progenitor species. Mol Biol Rep 46, 1227–1238 (2019). https://doi.org/10.1007/s11033-019-04591-3

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