Heterosis and combining ability in cytoplasmic male sterile and doubled haploid based Brassica oleracea progenies and prediction of heterosis using microsatellites

RESEARCH ARTICLE Heterosis and combining ability in cytoplasmic male sterile and doubled haploid based Brassica oleracea progenies and prediction of heterosis using microsatellites Saurabh Singh ID1, S. S. Dey ID1*, Reeta Bhatia2, Raj Kumar1, Kanika Sharma3, T. K. Behera1 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 1 Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India, 2 Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, India, 3 ICAR-Indian Agricultural Research Institute, Regional Station, Katrain, Kullu, Himachal Pradesh, India * Abstract OPEN ACCESS Citation: Singh S, Dey SS, Bhatia R, Kumar R, Sharma K, Behera TK (2019) Heterosis and combining ability in cytoplasmic male sterile and doubled haploid based Brassica oleracea progenies and prediction of heterosis using microsatellites. PLoS ONE 14(8): e0210772. https://doi.org/ 10.1371/journal.pone.0210772 Editor: Harsh Raman, New South Wales Department of Primary Industries, AUSTRALIA Received: December 26, 2018 Accepted: August 6, 2019 Published: August 19, 2019 Copyright: © 2019 Singh et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: Financial support was provided by the NAHEP/CAAST research grant by Indian Council of Agricultural Research. Competing interests: The authors have declared that no competing interests exist. In Brassica oleracea, heterosis is the most efficient tool providing impetus to hybrid vegetable industry. In this context, we presented the first report on identifying superior heterotic crosses for yield and commercial traits in cauliflower involving cytoplasmic male sterile (CMS) and doubled haploid (DH) lines as parents. We studied the suitability of genomicSSRs and EST-SSRs based genetic distance (GD) and agronomic trait based phenotypic distance (PD) for predicting heterosis in F1 hybrids using CMS and DH based parents. 120 F1 hybrids derived from 20Ogura based CMS lines and 6 DH based testers were evaluated for 16 agronomic traits along with the 26 parental lines and 4 commercial standard checks. The genomic-SSRs and EST-SSRs based genetic structure analysis grouped the 26 parental lines into 4 distinct clusters. The CMS lines Ogu118-6A, Ogu33A, Ogu34-1A were good general combiner for developing early maturity hybrids. The SCA effects were significantly associated with heterosis suggesting non-additive gene effects for the heterotic response of hybrids. Less than unity value of σ2A/D coupled with σ2gca/σ2sca indicated the predominance of non-additive gene action in the expression of studied traits. The correlation analysis of genetic distance with heterosis for commercial traits suggested that microsatellites based genetic distance estimates can be helpful in heterosis prediction to some extent. Introduction In the plant kingdom, the family Brassicaceae holds a great agronomic, scientific and economic significance and comprises of more than 372 genera and 4060 species [1]. Brassica oleracea (CC, 2n = 18) constitutes a diverse group of economically and nutritionally important morphotypes known as cole vegetables (kale, kohlrabi, cabbage, cauliflower, broccoli, brussels sprout) [2]. The Brassica vegetables are also termed as ‘super-food’ as they are vital source of secondary metabolites, antioxidants, vitamins and minerals [3, 4, 5, 6]. Among the cultivated PLOS ONE | https://doi.org/10.1371/journal.pone.0210772 August 19, 2019 1 / 26 Microsatellite based prediction of heterosis using doubled haploids based parental lines B. oleracea morphotypes, cauliflower (B. oleracea var. botrytis L.) is an important vegetable crop grown worldwide. Great efforts have been made to improve the productivity and quality of this crop because of its huge economic value and quality attributes [7]. The replacement of open-pollinated varieties with F1 hybrids become more pronounced in cole vegetables because of their high uniformity, better quality, tolerance to various biotic and abiotic stresses [5, 8]. The genetic mechanisms namely, sporophytic self-incompatibility (SI) and cytoplasmic malesterility (CMS) have been used widely in hybrid breeding programme of B. oleracea [5, 8, 9, 10, 11, 12]. However, frequent breakdown of self-incompatibility has been reported in Brassica vegetables due to the high temperature sensitivity of S-alleles. Thus, SI lines are not always stable and result in ‘sibbed’ seed in hybrid population [11]. Moreover, maintenance of S-allele lines is time-consuming and expensive. In snowball cauliflower, SI system is very poor or not present at all [11, 13]. Under these circumstances, the CMS provides a better alternative for the heterosis breeding in cole crops [5, 8, 14]. Heterosis or hybrid vigor, is manifested as superior performance of F1 hybrids as compared to the parents [15, 16, 17]. Heterosis is highly complex phenomenon and different hypothesis and genetic basis have been suggested to explain the basis of heterosis. [15, 16, 18, 19, 20]. Further, the application of genomics tools has suggested the role of epigenetic regulations in explaining the heterosis phenomenon across the crops [16, 17, 19, 20]. Proper selection of inbreds and identification of superior heterotic combinations is crucial for exploiting heterosis in crop improvement. The traditional approaches of quantitative genetics like diallel, generation mean, line × tester analysis and estimating genetic components revealing various gene effects are effective in unraveling genetic basis of heterosis [5, 15, 21, 22]. The measures of both general combining ability (GCA) and specific combining ability (SCA) are necessary for selection of parental lines to develop heterotic combinations [23]. Estimation of GCA provides information on breeding value and additive genetic variance while, SCA is associated with non-additive effects (dominance effects, additive×dominant, and dominant×dominant interactions). Among different biometrical approaches, line × tester analysis is very efficient for estimating GCA effects of lines and testers, SCA effects of cross combinations and revealing information about the nature of gene actions [8, 21, 24]. The extent of heterosis has been reported to vary with the mode of reproduction, genetic distance of parents, traits under investigation, developmental stage of plant and prevailing environment [23, 25, 26, 27, 28, 29]. The pair-wise parental GD has been suggested as a good indicator of per se hybrid performance and recognition of heterotic groups [23, 25, 26, 27, 28, 29]. Different approaches are available to determine genetic distance depending upon morphological traits, horticult (...truncated)