Agro-morphological and molecular diversity in different maturity groups of Indian cauliflower (Brassica oleracea var. botrytis L.)

Rakshita, K. N.; Singh, Shrawan Kumar; Verma, V. K.; Sharma, Brij Mohan; Saini, Neeru; Iquebal, Mir Asif; Sharma, Akanksha; Dey, S. S.; Behera, Tusar Kanti

doi:10.1371/journal.pone.0260246

Cited by 10 publications

(12 citation statements)

References 39 publications

(60 reference statements)

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“…Most of the 124 cultivars in Pop-3 were loose-curd cauli owers which mainly originated from the provinces of China such as Shanghai, Zhejiang, Fujian, and Taiwan. In previous studies, clusters with a composite pattern of genotype distribution [42]. Our results indicate that the discernibility of the core marker set is reliable, and the classi cation patterns of most studied cauli ower cultivars essentially corresponded to the geographic origin and degree of curd solidity.…”

Section: Discussionsupporting

confidence: 65%

Construction of a SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

Yang

et al. 2022

Preprint

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Cauliflower is one of the most important vegetable crops grown worldwide. However, efforts to improve cauliflower are hindered by the lack of genetic diversity information and efficient molecular markers. In this study, we aim to construct DNA fingerprints for 329 cauliflower cultivars based on SNP markers and the KASP system. After rigorous filtering, a total of 1,662 candidate SNPs were obtained from nearly 17.9 million SNP loci. The mean values of PIC, MAF, heterozygosity and gene diversity of these SNPs were 0.389, 0.419, 0.075, and 0.506, respectively. To generate ideal SNP marker sets from the candidates, we developed a program for in silico simulations on 153 core cauliflower germplasm samples. Finally, 41 highly polymorphic KASP markers were selected and applied in the identification of 329 cauliflower cultivars which were mainly collected from public market. Furthermore, based on the KASP genotyping data, we performed phylogenetic analysis and population structure analysis of the 329 cultivars. As a result, these cultivars could be classified into three major clusters, and the classification patterns were significantly related to their curd solidity and geographical origin. Finally, fingerprints of the 329 cultivars and 2D barcodes with genetic information of each sample were generated. The fingerprinting database developed in this study provides a practical tool for identifying the authenticity and purity of cauliflower seeds and valuable genetic information of the current cauliflower cultivars.

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Section: Discussionsupporting

confidence: 65%

Construction of a SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

Yang

et al. 2022

Preprint

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“…These intricacies and distortions give false information about genetic divergence. The assessment of genetic diversity through DNA markers offers a rapid and accurate method for assessing genetic diversity among genotypes [ 32 ] as they are independent of environment factors [ 46 ]. The use of DNA markers supports quick screening for polymorphic loci among diverse group of genotypes.…”

Section: Discussionmentioning

confidence: 99%

Morphological and molecular diversity in mid-late and late maturity genotypes of cauliflower

Rana,

Sharma,

Rana

et al. 2023

PLoS ONE

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Genetic diversity is the prerequisite for the success of crop improvement programmes. Keeping in view, the current investigation was undertaken to assess the agro-morphological and molecular diversity involving 36 diverse mid-late and late cauliflower genotypes following α-RBD design during winter season 2021–22. Six morphological descriptors predicted as polymorphic using Shannon diversity index with maximum for leaf margin (0.94). The genotypes grouped into nine clusters based on D2 analysis with four as monogenotypic and gross plant weight (32.38%) revealed maximum contribution towards the genetic diversity. Molecular diversity analysis revealed 2–7 alleles among 36 polymorphic simple sequence repeats (SSR) with average of 4.22. Primer BoESSR492 (0.77) showed maximum polymorphic information content (PIC) with mean of 0.58. SSR analysis revealed two clusters each with two subclusters with a composite pattern of genotype distribution. STRUCTURE analysis showed homogenous mixture with least amount of gene pool introgression within the genotypes. Thus, based on morphological and molecular studies, the diverse genotypes namely, DPCaCMS-1, DPCaf-W4, DPCaf-US, DPCaf-W131W, DPCaf-S121, DPCaf-18, DPCaf-13, DPCaf-29 and DPCaf-CMS5 can be utilized in hybridization to isolate potential transgressive segregants to broaden the genetic base of cauliflower or involve them to exploit heterosis.

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“…C Cumulative KASP marker efficiency compared with the 41 core markers for the 329 cultivars divided the accessions into 4 categories, whereas the clustering patterns did not match traits such as curd maturity, curd solidity or geographic origin [38]. Rakshita et al divided 96 genotypes of Indian cauliflower and related crops into 4 clusters with a composite pattern of genotype distribution [42]. Our results indicate that the discernibility of the core marker set is reliable, and the classification patterns of most studied cauliflower cultivars essentially corresponded to the geographic origin and degree of curd solidity.…”

Section: Discussionmentioning

confidence: 99%

Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

Yang

et al. 2022

BMC Plant Biol

View full text Add to dashboard Cite

Cauliflower is one of the most important vegetable crops grown worldwide. However, the lack of genetic diversity information and efficient molecular markers hinders efforts to improve cauliflower. This study aims to construct DNA fingerprints for 329 cauliflower cultivars based on SNP markers and the KASP system. After rigorous filtering, a total of 1662 candidate SNPs were obtained from nearly 17.9 million SNP loci. The mean values of PIC, MAF, heterozygosity and gene diversity of these SNPs were 0.389, 0.419, 0.075, and 0.506, respectively. We developed a program for in silico simulations on 153 core germplasm samples to generate ideal SNP marker sets from the candidates. Finally, 41 highly polymorphic KASP markers were selected and applied to identify 329 cauliflower cultivars, mainly collected from the public market. Furthermore, based on the KASP genotyping data, we performed phylogenetic analysis and population structure analysis of the 329 cultivars. As a result, these cultivars could be classified into three major clusters, and the classification patterns were significantly related to their curd solidity and geographical origin. Finally, fingerprints of the 329 cultivars and 2D barcodes with the genetic information of each sample were generated. The fingerprinting database developed in this study provides a practical tool for identifying the authenticity and purity of cauliflower seeds and valuable genetic information about the current cauliflower cultivars.

show abstract

Agro-morphological and molecular diversity in different maturity groups of Indian cauliflower (Brassica oleracea var. botrytis L.)

Cited by 10 publications

References 39 publications

Construction of a SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

Construction of a SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

Morphological and molecular diversity in mid-late and late maturity genotypes of cauliflower

Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

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