Identification and Characterization of Chickpea Genotypes for Early Flowering and High Seed Germination through Molecular Markers

Chickpea is the fourth most important legume crop contributing 3.1% to the total legume production and rich source of proteins, minerals and vitamins. Genetic diversity of wild and elite cultivar is quintessential for variety improvement. Determination of genetic diversity is more reliable and accurate, therefore, commonly used. In the present study, we analyzed the genetic diversity, population structure, cross-species transferability and allelic richness in 50 chickpea collection using 23 ISSR markers. The observed parameters such as allele number varied from 3 to 16,and polymorphic information content (PIC) varied from 0.15 to 0.4988, respectively. Further, range of allele size varied from 150 to 1600 bp, which shows the significance of ISSR markers for chickpea germplasm characterization. On the basis of ISSR marker genotypic data, dendrogram was constructed which divides these 50 chickpea in group I and II showing the reliability of ISSR markers. Among 50 chickpea, the accession P 74-1 is in group I and rest are in group II. Further we made mini-core collection of 15 diverse chickpea and sub-grouped them. Dendrogram, PCA, Dissimilarity matrix and Bayesian model based genetic clustering of 50 chickpea germplasms revealed that P 74-1 and P 1883are very diverse chickpea accession. Further selected 15 diverse chickpea screened for early flowering and high seed germination. Among 15 diversechickpea germplasms P 1857-1 and P 3971 has early flowering and high seed germination compared to P 1883 and other germplasm. Characterization of these diverse chickpea for early flowering and high seed germinationwould help in reducing crop duration and enhancing seed qualities. Utilization of these ISSRs markers in diversity analysis and population structure characterization of 50 chickpea germplasm suggests their wider efficacy for molecular breeding ofearly flowering and high seed germination.

Tapping Diversity From the Wild: From Sampling to Implementation

The diversity observed among crop wild relatives (CWRs) and their ability to flourish in unfavorable and harsh environments have drawn the attention of plant scientists and breeders for many decades. However, it is also recognized that the benefit gained from using CWRs in breeding is a potential rose between thorns of detrimental genetic variation that is linked to the trait of interest. Despite the increased interest in CWRs, little attention was given so far to the statistical, analytical, and technical considerations that should guide the sampling design, the germplasm characterization, and later its implementation in breeding. Here, we review the entire process of sampling and identifying beneficial genetic variation in CWRs and the challenge of using it in breeding. The ability to detect beneficial genetic variation in CWRs is strongly affected by the sampling design which should be adjusted to the spatial and temporal variation of the target species, the trait of interest, and the analytical approach used. Moreover, linkage disequilibrium is a key factor that constrains the resolution of searching for beneficial alleles along the genome, and later, the ability to deplete linked deleterious genetic variation as a consequence of genetic drag. We also discuss how technological advances in genomics, phenomics, biotechnology, and data science can improve the ability to identify beneficial genetic variation in CWRs and to exploit it in strive for higher-yielding and sustainable crops.

citSATdb: Genome-Wide Simple Sequence Repeat (SSR) Marker Database of Citrus Species for Germplasm Characterization and Crop Improvement

Microsatellites or simple sequence repeats (SSRs) are popular co-dominant markers that play an important role in crop improvement. To enhance genomic resources in general horticulture, we identified SSRs in the genomes of eight citrus species and characterized their frequency and distribution in different genomic regions. Citrus is the world’s most widely cultivated fruit crop. We have implemented a microsatellite database, citSATdb, having the highest number (~1,296,500) of putative SSR markers from the genus Citrus, represented by eight species. The database is based on a three-tier approach using MySQL, PHP, and Apache. The markers can be searched using multiple search parameters including chromosome/scaffold number(s), motif types, repeat nucleotides (1–6), SSR length, patterns of repeat motifs and chromosome/scaffold location. The cross-species transferability of selected markers can be checked using e-PCR. Further, the markers can be visualized using the Jbrowse feature. These markers can be used for distinctness, uniformity, and stability (DUS) tests of variety identification, marker-assisted selection (MAS), gene discovery, QTL mapping, and germplasm characterization. citSATdb represents a comprehensive source of markers for developing/implementing new approaches for molecular breeding, required to enhance Citrus productivity. The potential polymorphic SSR markers identified by cross-species transferability could be used for genetic diversity and population distinction in other species.

Development of KASP Markers for Germplasm Characterization and Fingerprinting Identification of Broccoli in China

Background: Broccoli (Brassica oleracea var. italica) is a vegetable widely cultivated in China. Many new-type broccoli cultivars were bred and developed by Chinese breeders during the recent three decades. However, the broccoli cultivar nomenclature and detailed information of genetic relationships among broccoli germplasms are unclear. Results: The present study identified millions of SNPs by next-generation sequencing of 23 representative broccoli lines. Through several steps of selection, 100 SNPs were successfully converted into KASP markers, and used to evaluate the genetic diversity, genetic relationship, and population structure of 392 broccoli accessions, which represent the mainly broccoli breeding materials in China. The initial, introduced and improved accessions were well clustered, though some accessions were overlapped between groups, probably reflecting the fact that breeding activities led to genetic similarities. To make the KASP genotyping more efficient and cost-effective, 25 of the 100 KASPs were selected for fingerprinting of all accessions, and the 2D barcode contained fingerprinting information were generated for elite varieties. Conclusion: The KASP markers developed in this study provided an efficient way for germplasm characterization, DNA fingerprinting, seed purity identification, and marker-assisted selection of broccoli in China.

Are there differences in heterozygosity of strains obtained from intercrossed and self-fertilized onion plants?

ABSTRACT The commercial use of onion hybrids is preferred by producers. In contrast, the production of hybrid onion seeds is extremely inefficient. This is due to the use of lineages obtained by successive self-fertilizations assuming the effect of inbreeding depression per se. Therefore, it is necessary to understand new alternatives to reduce the effect of inbreeding depression in the strains. The objective of this study was to evaluate possible differences in polymorphism and levels of heterozygosity of strains obtained from intercrossed and self-fertilized plants. Twelve onion populations belonging to Bayer’s breeding program (Granex, IPA-1, IPA-2 and IPA-3) were used, obtained by self-fertilization of one plant, intercrossing of two plants or intercrossing of three plants. Three individuals from each strain were used in the analyzes. The amplifications were performed using 8 microsatellite primers with greater polymorphism, according to germplasm characterization studies carried out by CITA. Heterozygosity generally decreases with self-fertilization and increases as more plants are used in the cross. The SSR markers used in the present study were efficient in detecting variability in different genetic backgrounds. With the results obtained, it is suggested to carry out the obtaining of hybrids between the different combinations and to analyze the performance per se of the different modalities of obtaining strains proposed in the present research.

Identification and preliminary characterization of early fruiting mangabeira (Hancornia speciosa – Apocynaceae)

The mangabeira (Hancornia speciosa G.) is a native Brazilian species in the process of domestication. It has several potential uses. In recent years the populations of mangabeira have become fragmented and, to conserve their genetic resources, Embrapa Tabuleiros Costeiros has, since 2006, maintained a Mangaba Genebank, which currently has 299 individuals distributed across 27 accessions. In one of these accessions (CP), first fruiting was observed to occur at 13 months, indicating precocity. The current project was developed with the intention of morphologically characterizing the CP accessions and evaluating the extent of genetic diversity between genotypes, based on genetic markers associated with fruiting precocity. Morphological variation in crown and leaf shape, growth habit, total height, stem diameter and canopy height were investigated. For molecular characterization, 18 CP accession genotypes were used, all from Sergipe State, Brazil, and 11 ISSR markers were studied that generated 62 fragments with 91.4% polymorphism. The fruits have physical and chemical characteristics suitable for in natura consumption and also for processing. UPGMA dendrogram analysis showed the genotypes CP2 and CP6 to be most similar and CP10 the most divergent within the CP accessions. The results showed the existence of polymorphism, and genetic divergence among genotypes, thus reinforcing the importance of constant germplasm characterization, which guarantees information on gene sources for future use, while providing information concerning potential parents that can be used in breeding programs as well as the identification of duplicates.

Combinations of distance measures and clustering algorithms in pepper germplasm characterization

ABSTRACT Characterization and evaluation of genotypes conserved in the germplasm banks have become of great importance due to gradual loss of genetic variability and search for more adapted and productive genotypes. This can be obtained through several ways, generating quantitative and qualitative data. Joint analysis of those variables may be considered a strategy for an accurate germplasm characterization. In this study we aimed to evaluate different clustering techniques for characterization and evaluation of Capsicum spp. accessions using combinations of specific measures for quantitative and qualitative variables. A collection of 56 Capsicum spp. accessions was characterized based on 25 morphoagronomic descriptors. Six quantitative distances were used [A1) average of the range-standardized absolute difference (Gower), A2) Pearson correlation, A3) Kulczynski, A4) Canberra, A5) Bray-Curtis, and A6) Morisita] combined with distance for qualitative data [Simple Coincidence (B1)]. Clustering analyses were performed using agglomerative hierarchical methods (Ward, the nearest neighbor, the farthest neighbor, UPGMA and WPGMA). All combined distances were highly correlated. UPGMA clustering was the most efficient through cophenetic correlation and 2-norm analyses, showing a concordance between the two methods. Six clusters were considered an ideal number by UPGMA clustering, in which Gower distance showed a better adjustment for clustering. Most combined distances using UPGMA clustering allowed the separation of the accessions in relation to species, using both quantitative and qualitative data, which could be an alternative for simultaneous joint analysis, aiming to compare different clusters.