Genetic diversity and population structure of sweet orange [Citrus sinensis (L.) Osbeck] germplasm of India revealed by SSR and InDel markers

Sweet orange (Citrus sinensis (L.) Osbeck) is an important commercial citrus fruit crop, cultivated in India and across the world. In India most of the cultivated sweet orange species were introduced varieties. In this study, we used two molecular markers, SSR and InDels, to understand the genetic diversity and population structure of seventy-two sweet orange genotypes. Genetic parameters consisted of a total number of alleles, a number of polymorphic alleles (effective alleles); genetic diversity (G.D.), expected heterozygosity (He), and the polymorphic information content (PIC) were calculated based on molecular data. Two dendrograms were constructed based on the InDels and SSR. In both the cases, they formed three major clusters showing various degrees of variations with respect to members of the clusters. Population structure analysis revealed the presence of two distinct subpopulations. Therefore, in order to address various challenges and develop sweet orange varieties with desirable traits, there is a need to broaden the genetic base of sweet orange through the intensive collection in the northeastern region. These results of intraspecific genetic variability of the collections will dictate the path for the sweet orange breeding and conservation programs in India.

Development of SSR Markers and Genetic Diversity Evaluation of Mycocentrospora Acerina Causing Round Spot of Panax Notoginseng in Yunan Province, China

Sanqi round spot, which is caused by Mycocentrospora acerina, is a destructive disease limits the production of Panax notoginseng in Yunnan province of China. However, the disease has not been studied comprehensively. In the current study, we identify M. acerina polymorphic microsatellite markers using CERVUS 3.0 and compare the genetic diversity of its isolates from P. notoginseng round spot using Simple Sequence Repeat (SSR) markers and polyacrylamide gel electrophoresis. Thirty-two SSR markers with good polymorphism were developed using MISA and CERVUS 3.0. The genetic diversity of 187 M. acerina isolates were evaluated using 14 representative SSR primers, and the polymorphic information content values of 14 sites ranged from 0.813 to 0.946, with a total of 264 alleles detected at 14 microsatellite loci. The average expected heterozygosity was 0.8967. The genetic diversity of M. acerina in Yunnan province does not reflect geographic specificity.

Characterization and Genetic Diversity of Taif Chicken Ecotype Using Dense Microsatellites Panel

The current study is the first comprehensive investigation to address the native chicken ecotypes of the Taif region to unravel the genetic diversity using a dense panel of 40 microsatellites (SSR). Blood samples were collected from 25 hens randomly sampled from a village farm at Taif governorate. A total of 147 alleles were detected, with an average of 3.7 alleles per locus. The overall mean of polymorphic information content (PIC) was 0.43. The average observed heterozygosity (Hobs) of 0.28 was lower than the expected heterozygosity (Hexp) of 0.48. Out of 40l ocionly11 loci showed insignificant deviation from Hardy Weinberg expectation. The ecotypes showed low genetic diversity (HS = 0.65) and a high level of inbreeding (FIS= 0.75). The high FIS is indicative of the endangerment potentiality of this ecotype. Nine SSR showed an inbreeding coefficient of one. The significant estimate of the inbreeding coefficient of the present study calls for an immediate breeding plan to preserve such endangered ecotypes. Results of the present study will provide an initial guide to design further investigations for the development of sustainable genetic improvement and conservation programs for the Taif ecotype genetic resources.

Search of the new SSR-loci of DNA for development of effective technology for soybean genotyping

Soybean is the major protein-oil crop of a huge economic importance. Currently, to describe the new cultivars being applied for a patent there are used the modern methods based on an analysis of microsatellite (SSR) loci of DNA. The purposes of this work were a search of the new microsatellite markers to optimize the existing technology of soybean cultivars certification and identification as well as selection of conditions for PCR analysis and to test them on cultivars from the VIR’s collection. Seven microsatellite loci demonstrated the high polymorphism level on soybean cultivars and located in the different chromosomes were chosen in the literary sources and librarian data bases. The optimal temperatures for annealing were selected empirically for all the pairs of SSR-markers. The results of DNA amplification of 20 soybean genotypes showed all seven studied SSR-loci were polyallel. In general, we revealed 22 alleles that on average are 3.1 per a locus. The effective number of alleles Ne for the studied soybean genotypes varied from 1.69 to 2.27 and on average was equal to 2.01. An average meaning of an index of the polymorphic information content (PIC) was 0.50. All the investigated soybean samples have the unique sets of alleles by the studied loci. Seven approbated loci can be used in development of an effective technology for identification and certification of the soybean genotypes.

Genetic structure and diversity among individuals of Copaifera langsdorffii Desf. from Mato Grosso, Brazilian Amazon, using ISSR markers

The Amazon is the largest tropical forest in the world and is home to around 20% of all the biodiversity on the planet, among the species present in the Amazon is Copaifera langsdorffii, exploited mainly for the extraction of oil-resin and wood, often in ways incorrect, which can cause the loss of genetic variability. The aim of this study was to evaluate the genetic structure and diversity among individuals of C. langsdorffii located in Mato Grosso, Brazil, using ISSR markers. We sampled leaves from 27 adult individuals of C. langsdorffii, whose total genomic DNA was extracted. A total of 12 ISSR primers were used for the molecular characterization of the individuals. A grouping analysis was performed using the unweighted pair group method, Bayesian analysis and characterized by the genetic diversity. The genetic diversity among and within the groups was demonstrated by the AMOVA. As a result, 106 fragments were amplified and 98.11% were polymorphic. The polymorphic information content of each primer ranged from 0.45 to 0.81. The dendrogram showed the formation of 4 distinct groups. The greatest genetic variability is found within the groups and not between them. The percentage of polymorphism, genetic dissimilarity values and genetic diversity indexes indicate that there is high genetic variability among Copaifera langsdorffii individuals, suggesting that ISSR primers were efficient in detecting polymorphism in this species and that the individuals have potential for compose programs aimed at the preservation of the species and the ability to integrate germplasm banks.

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.

Elucidating Genetic Diversity in Apricot (Prunus armeniaca L.) Cultivated in the North-Western Himalayan Provinces of India Using SSR Markers

Apricot (Prunus armeniaca L.) is an important temperate fruit crop worldwide. The availability of wild apricot germplasm and its characterization through genomic studies can guide us towards its conservation, increasing productivity and nutritional composition. Therefore, in this study, we carried out the genomic characterization of 50 phenotypically variable accessions by using SSR markers in the erstwhile States of Jammu and Kashmir to reveal genetic variability among accessions and their genetic associations. The genetic parameter results revealed that the number of alleles per locus (Na) ranged from 1 to 6 with a mean Na value of 3.89 and the mean effective number of alleles (Ne) per locus 1.882 with a range of 1.22 to 2. Similarly, the polymorphic information content (PIC) values ranged from 0.464 to 0.104. The observed heterozygosity (Ho) (0.547) was found to have higher than expected heterozygosity (He) (0.453) with average heterozygosity of 0.4483. The dendrogram clustered genotypes into three main clades based on their pedigree. The population structure revealed IV sub-populations with all admixtures except the III sub-population, which was mainly formed of exotic cultivars. The average expected heterozygosity (He) and population differentiation within four sub-populations was 1.78 and 0.04, respectively, and explained 95.0% of the total genetic variance in the population. The results revealed that the SSR marker studies could easily decrypt the genetic variability present within the germplasm, which may form the base for the establishment of good gene banks by reducing redundancy of germplasm, selection of parents for any breeding program.

Molecular Characterization of Drought Tolerant Genotypes of Pearl Millet [Pennisetum glaucum (L.) R. Br.] for A1 Zone

Pearl millet is a widely grown, climate resilient rainfed cereal crop cultivated on 29 million ha in the arid and semi-arid tropical regions of Asia and Africa accounting for almost half of global millet production. It is useful for minimizing the adverse effect of climate change, hence facilitating income and food security among farming communities. It has deep root system and exhibit climate-resilient features including adaptation to a wide range of ecological conditions, less irrigational requirements, better growth and productivity in low nutrient input conditions, less dependent on synthetic fertilizers and minimum vulnerability to environmental stresses and thus can survive in harsh climatic conditions, less fertile soil under water scarcity. Breeding of drought tolerant varieties and selecting genotypes for better water use efficiency is important in pearl millet to mitigate the changing climatic scenario. In this study, 24 genotypes of pearl millet which are drought tolerant and specific for A1 zone were characterized using 15 drought specific SSR primers. All the 15 SSRs amplified products of varying sizes ranging between 90-550 bp. A total of 40 alleles were obtained in this study and the number of alleles per locus varied between 2 to 5 with an average of 2.67 alleles. Polymorphic Information Content (PIC) varied from 0.34 to 0.76 with an average of 0.53 PIC value. This study will be useful for developing high yielding, dual purpose cultivars for low rainfall areas i.e. A1 zone and increasing pearl millet productivity.

Construction of a core collection of native Perilla germplasm collected from South Korea based on SSR markers and morphological characteristics

The leaves and seed oil of Perilla crop (Perilla frutescens L.) have attracted interest as health foods in East Asia. This crop has been traditionally cultivated and used for a long time as a folk plant, especially in Korea. In our study, the 22 SSR markers and eight morphological traits were used to assess the genetic diversity and population structure, to select a core collection of 400 Perilla accessions conserved in the RDA-Genebank of South Korea. A total of 173 alleles were detected and the number of alleles per locus ranged from 4 to 15 (average = 7.9). Gene diversity and polymorphic information content ranged from 0.138 to 0.868 (average = 0.567) and 0.134 to 0.853 (average = 0.522), respectively. The 400 accessions were not clearly distinguished geographically by STRUCTURE and UPGMA analyses. A core collection (44 accessions) was selected from the entire collection by using PowerCore. The core collection accounted for 11.0% of the entire Perilla collection, including 100% of the number of alleles maintained in the whole collection and with similar or greater Shannon–Weaver and Nei diversity indices than the whole collection. The core collection selected by SSR markers was evenly distributed in three clusters on a scatter plot by eight morphological traits. The first core collection of Perilla accessions was constructed, and it maintained allelic richness. Further modification of the core collection is expected with the continuous addition of new accessions of the two cultivated types of Perilla crop and their weedy types.

Genetic variability and population structure of Ethiopian chickpea (Cicer arietinum L.) germplasm

Evaluation of the genetic diversity and an understanding of the genetic structure and relationships of chickpea genotypes are valuable to design efficient germplasm conservation strategies and crop breeding programs. Information is limited, in these regards, for Ethiopian chickpea germplasms. Therefore, the present study was carried out to estimate the genetic diversity, population structure, and relationships of 152 chickpea genotypes using simple sequence repeats (SSR) markers. Twenty three SSR markers exhibited polymorphism producing a total of 133 alleles, with a mean of 5.8 alleles per locus. Analyses utilizing various genetic-based statistics included pairwise population Nei’s genetic distance, heterozygosity, Shannon’s information index, polymorphic information content, and percent polymorphism. These analyses exemplified the existence of high genetic variation within and among chickpea genotypes. The 152 genotypes were divided into two major clusters based on Nei’s genetic distances. The exotic genotypes were grouped in one cluster exclusively showing that these genotypes are distinct to Ethiopian genotypes, while the patterns of clustering of Ethiopian chickpea genotypes based on their geographic region were not consistent because of the seed exchange across regions. Model-based population structure clustering identified two discrete populations. These finding provides useful insight for chickpea collections and ex-situ conservation and national breeding programs for widening the genetic base of chickpea.