The genetic diversity and relationships of cauliflower (Brassica oleracea var. botrytis) inbred lines assessed by using SSR markers

Genomic analyses reveal the stepwise domestication and genetic mechanism of curd biogenesis in cauliflower

Cauliflower (Brassica oleracea L. var. botrytis) is a distinctive vegetable that supplies a nutrient-rich edible inflorescence meristem for the human diet. However, the genomic bases of its selective breeding have not been studied extensively. Herein, we present a high-quality reference genome assembly C-8 (V2) and a comprehensive genomic variation map consisting of 971 diverse accessions of cauliflower and its relatives. Genomic selection analysis and deep-mined divergences were used to explore a stepwise domestication process for cauliflower that initially evolved from broccoli (Curd-emergence and Curd-improvement), revealing that three MADS-box genes, CAULIFLOWER1 (CAL1), CAL2 and FRUITFULL (FUL2), could have essential roles during curd formation. Genome-wide association studies identified nine loci significantly associated with morphological and biological characters and demonstrated that a zinc-finger protein (BOB06G135460) positively regulates stem height in cauliflower. This study offers valuable genomic resources for better understanding the genetic bases of curd biogenesis and florescent development in crops.

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

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.

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

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.

Photosynthetic Efficiency and Glyco-Metabolism Changes in Artificial Triploid Loquats Contribute to Heterosis Manifestation

Previous studies indicated that extensive genetic variations could be generated due to polyploidy, which is considered to be closely associated with the manifestation of polyploid heterosis. Our previous studies confirmed that triploid loquats demonstrated significant heterosis, other than the ploidy effect, but the underlying mechanisms are largely unknown. This study aimed to overcome the narrow genetic distance of loquats, increase the genetic variation level of triploid loquats, and systematically illuminate the heterosis mechanisms of triploid loquats derived from two cross combinations. Here, inter-simple sequence repeats (ISSRs) and simple sequence repeats (SSRs) were adopted for evaluating the genetic diversity, and transcriptome sequencing (RNA-Seq) was performed to investigate gene expression as well as pathway changes in the triploids. We found that extensive genetic variations were produced during the formation of triploid loquats. The polymorphism ratios of ISSRs and SSRs were 43.75% and 19.32%, respectively, and almost all their markers had a PIC value higher than 0.5, suggesting that both ISSRs and SSRs could work well in loquat assisted breeding. Furthermore, our results revealed that by broadening the genetic distance between the parents, genetic variations in triploids could be promoted. Additionally, RNA-Seq results suggested that numerous genes differentially expressed between the triploids and parents were screened out. Moreover, KEGG analyses revealed that “photosynthetic efficiency” and “glyco-metabolism” were significantly changed in triploid loquats compared with the parents, which was consistent with the results of physiological indicator analyses, leaf micro-structure observations, and qRT-PCR validation. Collectively, our results suggested that extensive genetic variations occurred in the triploids and that the changes in the “photosynthetic efficiency” as well as “glyco-metabolism” of triploids might have further resulted in heterosis manifestation in the triploid loquats.

Morpho-molecular genetic diversity and population structure analysis in garden pea (Pisum sativum L.) genotypes using simple sequence repeat markers

Garden pea (Pisum sativum L.) is a self-pollinated plant species which played an important role for the foundation of modern genetics. Genetic diversity among 56 garden pea genotypes was assessed using 12 morphological descriptors, 19 quantitative traits and 8 simple sequence repeat (SSR) markers. Eight morphological descriptors were found polymorphic, and highest Shannon diversity index was recorded for pod curvature (1.18). Mahalanobis D2 illustrating genetic divergence arranged 56 genotypes into six clusters, with the highest inter-cluster distance between clusters IV and VI (18.09). The average values of Na (number of alleles), Ne (effective number of alleles), I (Shannon's Information index), PIC (polymorphism information content), Ho (observed heterozygosity) and He (expected heterozygosity) were 3.13, 1.85, 0.71, 0.36, 0.002 and 0.41, respectively. Pair wise genetic distance among all pairs of the genotypes varied from 0.33 to 1.00 with an average of 0.76. Based on genetic distance, the genotypes were classified into two main clusters (A and B) by cluster analysis, whereas structure analysis divided the genotypes into four sub-populations. The SSR makers indicated that present of genetic variability among the studied genotypes. When, we compared the groups formed by agro-morphological and molecular data, no genotypes were observed, indicating that both stages of characterization are crucial for a better understanding of the genetic variability. Hybridization between genetically diverse genotypes can be exploited to expend the genetic variability and introduce new traits in the pea breeding program.

Molecular characterization and genetic diversity analysis in Indian mustard (Brassica juncea L. Czern & Coss.) varieties using SSR markers

In this study, we evaluated genetic diversity in a panel of 87 Indian mustard varieties using 200 genomic-SSR markers. A total of 189 SSRs resulted into positive amplification with 174 (92.06%) SSRs generating polymorphic products and 15 (7.94%) SSRs producing monomorphic amplicons. A total of 552 alleles were obtained and allele number varied from 2–6 with an average number of 3.17 alleles per SSR marker. The major allele frequency ranged from 0.29 (ENA23) to 0.92 (BrgMS841) with an average value of 0.58 per SSR locus. The polymorphic information content (PIC) value ranged from 0.10 (BrgMS841) to 0.68 (BrgMS519) with 0.39 as mean PIC value. The gene diversity per locus ranged from 0.13 (BrgMS841) to 0.72 (ENA23 & BrgMS519) with a mean value of 0.48 per SSR primer pair. Both Unweighted Neighbor Joining-based dendrogram and population structure analysis divided all the 87 varieties into two major groups/subpopulations. Analysis of molecular variance (AMOVA) inferred the presence of more genetic variation (98%) among individuals than among groups (2%). A total of 31 SSRs produced 36 unique alleles for 27 varieties which will serve as unique DNA-fingerprints for the identification and legal protection of these varieties. Further, the results obtained provided a deeper insight into the genetic structure of Indian mustard varieties in India and will assist in formulating future breeding strategies aimed at Indian mustard genetic improvement.

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

The present study analysed the molecular and agro-morphological diversity in a set of 92 diverse cauliflower genotypes and two each of cabbage and broccoli. Field evaluation of the genotypes was done in randomized block design (RBD) at two locations (i.e. IARI, New Delhi and ICAR-RC-NEH Region, Barapani) during Rabi2019-20. Genotypes showed variation for all the eight observed traits at both locations and, the differences in early and snowball groups were distinct. Pusa Meghna, DC-33-8, Pusa Kartiki and CC-14 were earliest for curd initiation. Genotypes showed higher values for curd traits at Delhi. Molecular diversity was detected with 90 polymorphic simple sequence repeats (SSR). Number of alleles ranged from 1 to 9 with mean value of 2.16 and the highest polymorphic information content (PIC) value was observed for primer BoGMS0742 (0.68) with a mean value of 0.18. Cluster analysis using agro-morphological traits substantiated classification of the genotypes for maturity groups. However, SSR analysis revealed four clusters and with a composite pattern of genotype distribution. STRUCTURE analysis also supported the admixture and four subpopulations. The studyindicates for introgression of genetic fragments across the maturity groups, thereby, potential for use in further genetic improvement and heterosis breeding.

Understanding population structure and detection of QTLs for curding-related traits in Indian cauliflower by genotyping by sequencing analysis

Curd initiation and development are complex traits and highly responsive for different temperature ranges in cauliflower. The present study was aimed to identify QTLs for eight traits associated with curding behaviour in diverse germplasm of Indian cauliflower. For this, 92 genotypes of cauliflower and 2 each of tropical broccoli and cabbage were genotyped through genotyping by sequencing (GBS). It generated ≈302 million reads (9.1226E + 10 bp) and identified 35,381 SNPs, maximum from chromosome 3 (4735) with a mean value of 3981.1 SNPs. Ts/Tv ratio was 1.74, suggesting transition bias. STRUCTURE analysis revealed delta value of K = 4 and four subpopulations and prominence of population admixture. In total, 121 significant SNPs were detected for eight traits, 38 for Delhi (North Indian plain) and 83 for Barapani (North-East India). Twelve QTLs were detected for traits associated with regulation of curd formation and development, five of which were for marketable curd length, curd width, days to 50% curd harvest and marketable curd weight from Delhi region and seven for curd length, curd width, days to 50% curd harvest, gross plant weight, leaf length, marketable/net curd weight and number of leaves per plant for Barapani area of North East India. The SNPs identified will be useful for development of markers for curding-related traits and their use in breeding varieties with wider curding plasticity.

Molecular Breeding Strategy and Challenges Towards Improvement of Downy Mildew Resistance in Cauliflower (Brassica oleracea var. botrytis L.)

Cauliflower (Brassica oleracea var. botrytis L.) is one of the important, nutritious and healthy vegetable crops grown and consumed worldwide. But its production is constrained by several destructive fungal diseases and most importantly, downy mildew leading to severe yield and quality losses. For sustainable cauliflower production, developing resistant varieties/hybrids with durable resistance against broad-spectrum of pathogens is the best strategy for a long term and reliable solution. Identification of novel resistant resources, knowledge of the genetics of resistance, mapping and cloning of resistance QTLs and identification of candidate genes would facilitate molecular breeding for disease resistance in cauliflower. Advent of next-generation sequencing technologies (NGS) and publishing of draft genome sequence of cauliflower has opened the flood gate for new possibilities to develop enormous amount of genomic resources leading to mapping and cloning of resistance QTLs. In cauliflower, several molecular breeding approaches such as QTL mapping, marker-assisted backcrossing, gene pyramiding have been carried out to develop new resistant cultivars. Marker-assisted selection (MAS) would be beneficial in improving the precision in the selection of improved cultivars against multiple pathogens. This comprehensive review emphasizes the fascinating recent advances made in the application of molecular breeding approach for resistance against an important pathogen; Downy Mildew (Hyaloperonospora parasitica) affecting cauliflower and Brassica oleracea crops and highlights the QTLs identified imparting resistance against this pathogen. We have also emphasized the critical research areas as future perspectives to bridge the gap between availability of genomic resources and its utility in identifying resistance genes/QTLs to breed downy mildew resistant cultivars. Additionally, we have also discussed the challenges and the way forward to realize the full potential of molecular breeding for downy mildew resistance by integrating marker technology with conventional breeding in the post-genomics era. All this information will undoubtedly provide new insights to the researchers in formulating future breeding strategies in cauliflower to develop durable resistant cultivars against the major pathogens in general and downy mildew in particular.

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

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 genomic-SSRs 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 σ²_gca/σ²_sca 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.