Genetic Variation of Lentil Landraces Across Different Altitudes in Azerbaijan

The aim of this study is investigation the applicability of SSR and ISSR markers in evaluating the genetic relationships in twenty accessions ofAegilopsandTriticumspecies with D genome in different ploidy levels. Totally, 119 bands and 46 alleles were detected using ten primers for ISSR and SSR markers, respectively. Polymorphism Information Content values for all primers ranged from 0.345 to 0.375 with an average of 0.367 for SSR, and varied from 0.29 to 0.44 with the average 0.37 for ISSR marker. Analysis of molecular variance (AMOVA) revealed that 81% (ISSR) and 84% (SSR) of variability was partitioned among individuals within populations. Comparing the genetic diversity ofAegilopsandTriticumaccessions, based on genetic parameters, shows that genetic variation ofAe. crassaandAe. tauschiispecies are higher than other species, especially in terms of Nei’s gene diversity. Cluster analysis, based on both markers, separated total accessions in three groups. However, classification based on SSR marker data was not conformed to classification according to ISSR marker data. Principal co-ordinate analysis (PCoA) for SSR and ISSR data showed that, the first two components clarified 53.48% and 49.91% of the total variation, respectively. This analysis (PCoA), also, indicated consistent patterns of genetic relationships for ISSR data sets, however, the grouping of accessions was not completely accorded to their own geographical origins. Consequently, a high level of genetic diversity was revealed from the accessions sampled from different eco-geographical regions of Iran.

The present investigation has been undertaken with the objective to study the genetic variability and diversity among the Naga king chilli genotypes using SSR marker at Medziphema during kharif season of 2018. All total 89 bands were produced by 30 primers, 37 bands being polymorphic and producing average percentage polymorphic bands of 41.66 %. The Primer CAMS-826 showed highest percentage of polymorphic bands (75%), followed by primer CAMS 032, CAMS-117, CAMS- 864 and CAMS-647 which revealed (66.66 %) and primer CAeMS 009, CAMS 163, CAMS 871, HmpsE 047 AND HpmsE 014 exhibited 50% polymorphism which indicates that the primer can be used for genetic diversity study of C. chinense genotypes. Genetic parameters analyzed using Popgene® software indicated that Peren population has higher diversity among the four region populations. Jaccard’s similarity coefficient between the genotypes ranged from 0.64 to 0.96, indicating moderate variation between the genotypes. Clustering analysis depicted three clusters where germplasm collected from Peren and Medziphema showed close relatedness and Principal Coordinate Analysis (PCo A) plot obtained also supports cluster analysis data. Germplasm evaluation is of immense important for genetic crop improvement.

Sustainable use of Genetic Diversity in Forage and Turf Breeding

The molecular genetic diversity of 404 indigenous landraces from sesame core collection in China were evaluated by 11 SRAP and 3 SSR markers, 175 fragments were generated, of which 126 were polymorphic with an average polymorphism rate of 72%. Jaccard’s genetic similarity coefficients (GS=0.7130), Nei’s gene diversity (h=0.2418) and Shannon’s Information index (I=0.3847) were calculated, a dendrogram of the 404 landraces was made, landraces from various zones were distributed throughout the dendrogram, accessions from different agro-ecological zones were indistinguishable by cluster analysis, geographical separation did not generally result in greater genetic distance, a similar pattern was obtained using principal coordinates (PCO) analysis. As to seven agro-ecological zones, the maximum Nei’s gene diversity (h = 0.2613) and Shannon index (I = 0.3980) values in zone VII indicated that they were genetically more diverse than those in other zones, while the least genetically diverse region was zone III (h = 0.1772, I = 0.2858). Nei’s genetic identity and genetic distance among landraces from seven agro-ecological zones were also analyzed, the genetic relationship of seven zones was inferred using the UPGMA method. This study demonstrated that SRAP and SSR markers were appropriate for evaluation of sesame genetic diversities. There existed extensive genetic diverse among indigenous landraces and the abundance of genetic diversity of landraces in different agro-ecological zones was various. Understanding of these characteristics of indigenous landraces in China can provide theoretical foundation for further collection, effective protection and reasonable utilization of these sesame landraces in breeding.

Assessing genetic diversity and building a core collection is essential to advancing tea plant breeding. In this study, ten SSR markers exhibiting robust amplification and polymorphism were employed to genotype 292 tea accessions sourced from various regions in Huangshan city. The results revealed significant genetic variation, encompassing 180 alleles. Genetic structure was evaluated using neighbor-joining clustering, principal coordinate analysis, and Structure analyses, which categorized the tea accessions into two primary clusters. The genetic diversity within these clusters demonstrated high similarity, likely due to their close geographical proximity. A core collection was established utilizing Core Hunter software, resulting in the selection of 35% of the accessions to effectively represent the genetic diversity of the entire collection. This core collection comprises 102 tea accessions, preserving a high percentage of allele richness and genetic diversity. This research offers valuable insights into genomics research and the sustainable management of tea plant genetic resources in Huangshan city.

Lentil (Lens culinaris Medik.) is commonly grown in drought-prone areas where terminal heat and drought are frequent. The limited-transpiration (TRlim) trait under high vapor pressure deficit (VPD) could be a way to conserve water and increase yield under water deficit conditions. The TRlim trait was examined in cultivated and wild lentil species together with its evolution throughout the breeding pipeline. Sixty-one accessions representing the six wild lentil species (L. orientalis, L. tomentosus, L. odemensis, L. lamottei, L. ervoides, and L. nigricans) and 13 interspecific advanced lines were evaluated in their transpiration response to high VPD. A large variation in transpiration rate (TR) response to increased VPD was recorded among wild lentil accessions, with 43 accessions exhibiting a breakpoint (BP) in their TR response to increasing VPD, with values ranging from 0.92 kPa to 3.38 kPa under greenhouse conditions. Ten genotypes for the interspecific advanced lines displayed a BP with an average of 1.95 kPa, much lower than previously reported for cultivated lentil. Results from field experiments suggest that the TRlim trait (BP=0.97 kPa) positively affected yield and yield-related parameters during the years with late-season water stress. The selection of TRlim genotypes for high VPD environments could improve lentil productivity in drought-prone areas.

Background and Aims. Vitis vinifera L. is a major global horticulture crop which holds historical connections contributing to the development of human culture. The main objective of the study was to explore the genetic diversity and structure of grapes curated at the germplasm bank of Aragón and link them to cultivar utilization, putative geographic origin, and historical events. Methods and Results. The genetic diversity of the 411 accessions of the Grapevine Germplasm Bank was assessed using 26 SSR markers. SSR markers VVIP31, VMC4F3-1, VVIV67, and VVS2 distinguished the 156 nonredundant genotypes found in the collection. The profiles were compared to the El Encin database, and 105 were identified as known cultivars, of which 93 were Spanish, 12 were from other European origins, and 51 others were not known. The 51 profiles, as they were all collected in Spain, were designated as Spanish unknown for further analysis. To establish a comparative study for principal coordinate analysis (PCoA) and structure, we kept 113 identified genotypes from this collection but added 61 representative genotypes with diverse European and oriental origins. Bayesian analysis and PCoA showed four distinct groups of grape cultivars: (1) traditional Spanish wine grape from Aragón or cultivated along the Ebro River, (2) Spanish wine grape, (3) Spanish and oriental table grape, and (4) Italian, Portuguese, French, and German-Slovenian wine grape varieties. Conclusions. The 51 unknown Spanish genotypes were not registered yet in any European commercial list and are of special interest. These genotypes could be ancient cultivars adapted to local climatic and environmental conditions and probably resilient to face the new conditions derived from climate change.

Sponge gourd (Luffa cylindrica) is a versatile economic crop with nutritional, medicinal, and industrial value, but its genetic research has long been limited by a lack of stable molecular markers. Although high-quality genomic data of the sponge gourd line P93075 is available, no comprehensive whole-genome simple sequence repeat (SSR) marker development and systematic genetic diversity analysis based on this genome have been reported to date. This study first developed SSR markers using the high-quality L. cylindrica P93075 genome as reference. Using a microsatellite identification tool (MISA), 128,557 genome-wide SSR loci were identified, with a density of 195.91 SSRs/Mb; dinucleotide repeats (41.25% of total loci) were the dominant type. Candidate polymorphic SSR markers were initially screened via TBtools, resulting in 8,557 potential polymorphic markers. These markers showed ≥3 bp differences in amplified fragment length between the P93075 and SG2019 genomes. For validation, 308 randomly selected markers evenly distributed across 13 chromosomes were tested by polyacrylamide gel electrophoresis (PAGE), with 232 showing clear polymorphism, corresponding to a 75.32% polymorphism rate. In this study, 15 highly polymorphic SSR markers with a mean polymorphism information content (PIC) of 0.6838 were employed to analyze the genetic diversity and population structure of 67 globally sourced sponge gourd germplasms. The analysis revealed high genetic diversity, with an average gene diversity of 0.7267 and an average Shannon-Weaver index of 1.4618. Population structure analysis using Structure 2.3.4, together with unweighted pair group method with arithmetic mean (UPGMA) clustering and principal coordinate analysis (PCoA), consistently grouped the 67 germplasms into three groups. The clustering pattern was closely correlated with geographical origin. Based on these analyses, India was identified as the core genetic diversity center of sponge gourd in this study, consistent with previous domestication research findings. These newly developed SSR markers and insights into genetic diversity fill the gap of genome-wide SSR resources for sponge gourd and provide a solid foundation for sponge gourd molecular breeding, germplasm utilization, and genetic research.

A comprehensive evaluation of genetic diversity in persimmon (Diospyros kaki Thunb.) germplasms based on large-scale morphological traits and SSR markers

Amomum villosum, serving as an important medicinal material, is complex in the genetic background of germplasm resources. Exploring the genetic diversity and genetic relationship of germplasm resources is conducive to clarifying the germplasm source and genetic background of A. villosum, so as to improve the efficiency of parent selection and variety breeding of A. villosum. Seventy-one pairs of SSR primers were used for PCR amplification of 84 A. villosum samples by polyacrylamide gel electrophoresis. Fifty-four pairs of SSR primers with high polymorphism were screened out for the analysis of genetic diversity. The results showed that 293 alleles were detected from 84 germplasm resources by 54 pairs of SSR primers, with an average of 5.32 alleles for each pair of primers, and a variation range of 3-8, and the primer AVL12 marked the highest number of alleles. The PIC value of each locus varied from 0.068 7 to 0.828 9, with an average of 0.529 9, and the highest was marked by AVL24. The genetic diversity of A. villosum was the highest in Yunnan, followed by Guangxi, and the lowest was found in Guangdong. The population structure analysis and cluster analysis showed that the samples were classified into two groups. In terms of origin, samples from Yunnan and Guangxi had a close genetic relationship, and there was no obvious differentiation of A, villosum resources from different origins. In this study, 54 pairs of SSR markers were used to analyze the genetic diversity and population structure of 84 germplasm resources, which can reflect the genetic relationship between A. villosum samples from different germplasm sources and different populations, thus providing a theoretical basis for the collection, research, and breeding of A. villosum resources.

Genetic Diversity Among Chinese Pea ( Pisum sativum L.) Landraces as Revealed by SSR Markers

The genus Passiflora encompasses many species that are endemic to the Brazilian territory, including some with economic value. Studies on genetic diversity in this genus are fundamental because they allow understanding genetic variability and distance. The present study aimed to determine the genetic variability and distances among 10 species of the genus Passiflora by using microsatellite markers (Simple Sequence Repeat, SSR). Twenty-eight heterologous microsatellite markers were tested, but only 12 were used in the diversity analysis because they amplified in at least 80% of the species. A clear separation was observed among the subgenuses studied, as well as wide variation among the accessions of Passiflora. This knowledge enables breeders to explore diversity and transfer favorable alleles found in wild species.

The assessment of genetic diversity and structuration of germplasm is essential for the efficient organization of breeding material. The objectives of the study were to (i) examine the population structure of elite sugar beet germplasm, (ii) investigate genetic diversity within and among subgroups of elite sugar beet germplasm, and (iii) assess the extent of linkage disequilibrium (LD) within elite sugar beet germplasm. A total of 111 and 178 inbred lines from the seed and pollen parent (SP and PP) heterotic gene pools, respectively, which had been genotyped with 23 SSR markers, were used in this study. Two distinct subgroups were detected within the entire germplasm set by STRUCTURE and principal coordinate analysis (PCoA). This observation was not expected because the SP heterotic pool of sugar beet was developed out of the PP heterotic pool in the late 1970s. Our observation of high LD in elite sugar beet germplasm suggests that association mapping will be possible in the examined germplasm set using a relatively low numbers of markers. However, to reduce the problem of false-positive marker-phenotype association, it might be necessary to examine the subgroups separately or apply association mapping methods which take into account this structure.

Information on diversity of genetic materials is vital for choosing parents in a breeding program. The objective of the study was to determine the pattern and level of genetic diversity among the selected 20 tetraploid potato genotypes using 16 SSR markers to identify suitable parents for breeding purposes. The microsatellites showed considerable variation among genotypes and sixty four alleles were amplified by the 16 primer pairs. The number of polymorphic alleles per locus ranged from 2 to 8 with an average of 3.9. The highest number of null alleles was observed was six for genotype Nakpot1. The overall size of the amplified product varied from 48 bp (marker STI0023) to 309 bp (marker STM5121). PIC values ranged from 0.0948 to 0.7832, with an average of 0.4307 per locus. Heterozygosity values ranged from 0.0997 to 0.805 with an average of 0.466919. Significant positive linear correlations were observed between PIC values and number of alleles (r = 0.905); and heterozygosity and number of alleles (r = 0.8659) at p < 0.001. Cluster analysis separated the genotypes into three different groups. The genetic distance between clones ranged from 1 to 5.7. Cruza had the highest genetic distance while the shortest genetic distance was observed between 396026.103 and 396034.104. The microsatellites used in this study provided useful information regarding the variability of the tested genotypes and their selection for breeding purposes.

In theoretical biology, a prevailing hypothesis posits a profound interconnection between effective population size (Ne), genetic diversity, inbreeding, and genetic load. The domestication and improvement processes are believed to be pivotal in diminishing genetic diversity while elevating levels of inbreeding and increasing genetic load. In this study, we performed a whole genome analysis to quantity genetic diversity, inbreeding, and genetic load across seven wild Ovis species and five domesticated sheep breeds. Our research demonstrates that the genetic load and diversity of species in the genus Ovis have no discernible impact on recent Ne, and three species within the subgenus Pachyceros tend to carry a higher genetic load and lower genetic diversity patterns. The results coincide with these species' dramatic decline in population sizes within the subgenus Pachyceros ~80-250 thousand years ago. European mouflon presented with the lowest Ne, lower genetic diversity, and higher individual inbreeding coefficient but a lower genetic load (missense and LoF). This suggests that the small Ne of European mouflon could reduce harmful mutations compared to other species within the genus Ovis. We showed lower genetic diversity in domesticated sheep than in Asiatic mouflon, but counterintuitive patterns of genetic load, i.e., lower weak genetic load (missense mutation) and no significant difference in strong genetic load (LoF mutation) between domestic sheep and Asiatic mouflon. These findings reveal that the "cost of domestication" during domestication and improvement processes reduced genetic diversity and purified weak genetic load more efficiently than wild species.