Polymorphic SSR Markers Research Articles

Genetic diversity analysis of indigenous pomegranate (Punica granatum L.) germplasm lines

Pomegranate (Punica granatum L.) is an ancient edible fruit crop well recognized for its immense nutraceutical and medicinal properties. Precise morphological characterization of wild, exotic and commercial (cultivar) varieties and understanding the molecular variability in perennial crops like pomegranate is essential for developing varietal DNA fingerprints, identifying true-to-type of genotypes, to avoid duplication and overcome the problem of clonal admixture. It has become a challenge to identify varieties based solely on observable phenotypic traits due to dynamic environmental factors that influence physical traits and increasing number of varieties. Hence, the implementation of stable molecular markers is the best complementary biotechnological tool, which fulfil the above requirements. In our first objective, we identified 24 polymorphic SSR markers out of 40. These SSRs screened on 13 different varieties of pomegranate. The PIC value ranged from 0.13 to 0.37 (mean 0.25) and heterozygosity percent ranged from 0.14% to 0.50% (mean 0.35%). Highest PIC value and heterozygosity observed in PgSSR78 marker. Similarity coefficient matrix showed the genetic distance between the twenty-four varieties, ranged from 0.58 to 0.99. Maximum similarity was observed between Alah and Khandari. Minimum similarity was found between IC318743 and 1185 followed by Maha and 1185. PgSSR16, PgSSR23, PgSSR49, PgSSR60, PgSSR32, PgSSR40, PgSSR78 markers were found with high PIC value and heterozygosity and these primers could be useful for pomegranate cultivar identification. From this study, microsatellite markers have proven to be very useful marker for developing varietal identification marker at early growth stage due to its high polymorphism, abundance, multi-allelic and co-dominant inheritance

Genetic Relationships of Indigenous King Coconut (Cocos nucifera L.) Populations as Determined by SSR Markers

King Coconut (KC) is an indigenous and highly valuable germplasm resource in Sri Lanka. Yet, KC populations' genetic diversity, relationships, and conservation strategies are not fully understood. Indigenous old KC populations have been dispersed across a few ancient villages in Sri Lanka. Five geographically dispersed locations were selected in Sri Lanka, and 20 KC individuals from each location were collected for the current study. Six randomly selected samples from every geographical location, together with the standard two Sri Lanka Red Dwarf and two Sri Lanka Tall varieties were initially genotyped using 21 SSR markers for polymorphism. Based on the results, ten polymorphic SSR markers were selected and used for genotyping. Power Marker, STRUCTURE, and GenAlex software were used for the SSR genetic analysis. Results revealed 0.62 mean Gene Diversity (Hs), 4.2 mean allele number, and 0.55 polymorphic information content (PIC). Clear differentiation of populations was observed with the STRUCTURE and UPGMA dendrogram. Single branching in the UPGMA dendrogram for Anuradhapura and Marandawila KC populations revealed high genetic uniformity over multi-branched Kadugannawa and Colambageara populations. According to AMOVA, 64% of the genetic variation has been partitioned among populations, indicating moderate population differentiation. Detail analysis, including a higher number of KC populations and systematic molecular analysis using more SSRs/SNPs needed in the future before implementing conservation and utilization strategies.

Morpho-genetic assessment and dissecting the genetic architecture for Cercospora leaf spot (CLS) resistance in mung bean [Vigna radiata (L.) Wilczek

Cercospora leaf spot (CLS) has a substantial negative impact on mung bean production across the world. It is crucial to identify and incorporate alleles that might be helpful in combating CLS in order to maintain mung bean health, and productivity. Therefore, 90 mung bean genotypes, including four check varieties, and 66 polymorphic SSR markers were included in the present study during pre-rabi 2018 and pre-rabi 2019. Morpho-genetic analysis revealed a higher value of GCV for yield, cluster and pod numbers per plant, and plant height. All traits had excellent genetic advance (GA), with the exception of the number of seeds per pod, which was medium. PCA was used to separate up to 85.656 % of the variation in the characteristics between the two primary PCs. Molecular dissection revealed, the markers CEDG118 and CEDG074 to yield more genetic diversity, followed by CEDG073, CEDG030 and CEDG147. Estimation of allele frequencies revealed some alleles of the markers found linked to CLS resistance, i.e., CEDG001 (111 bp and 135 bp), CEDG006 (135 bp), CEDG153 (117 bp), CEDG210 (193 bp), CEDG117 (112 bp), CEDG020 (143 bp), CEDG067 (93 bp), CEDG146 (111 bp), and CEDG071 (231 bp and 267 bp). The highest private allelic frequency was employed by the markers CEDG153 and CEDG146. The dendrogram divided the panel population into two major clusters. However, two distinct genetic structure were found within the population. According to these findings, the mung bean germplasm panel used in the present study may have the ability to improve the local gene pool and aid in the development of CLS resistance breeding strategies using genomic tools and techniques.

Sources of genetic resistance to Fusarium wilt (Fusarium oxysporum f. sp tracheiphilum) in cowpea (Vigna unguiculata (L.) Walp.) and comparison of inoculum concentration levels

Fusarium wilt caused by Fusarium oxysporum f. sp tracheiphilum (Fot) is a soil-borne fungal disease of significant constraint to cowpea production in West Africa. The disease infection can cause up to 100% yield loss in highly infested fields. The most effective control strategy is the use of resistant varieties. Sixty cowpea germplasm collections were screened for resistance to F. oxysporum. The result revealed that only two (TVu 134 and TVu 410) of the germplasm showed a high level of resistance when subjected to artificial epiphytotic and innovative seedling root dip screening methods using three inoculum concentration levels. These two cultivars can be used directly by farmers or as potential donors for developing resistant cultivars against F. oxysporum. The study also identified useful polymorphic SSR markers associated with resistant and susceptible parents, which will significantly enhance the breeding programs in developing varieties’ resistance to the disease.

Deciphering the genetic diversity and population structure of wild barley germplasm against corn leaf aphid, Rhopalosiphum maidis (Fitch)

Corn-leaf aphid (CLA-Rhopalosiphum maidis) is a major insect pest of barley (Hordeum vulgare) causing yield loss upto 30% under severe infestation. Keeping in view of the availability of very few sources of CLA resistance in barley, the present investigation was framed to assess the genetic diversity and population structure of 43 wild barley (H. vulgare subsp. spontaneum) genotypes using eight microsatellite markers against R. maidis. Three statistical methods viz. multivariate-hierarchical clustering, Bayesian clustering and PCoA, unanimously grouped genotypes into three subpopulations (K = 3) with 25.58% (SubPop1-Red), 39.53% (SubPop2-Green) and 34.88% (SubPop3-Blue) genotypes including admixtures. Based on Q ≥ 66.66%, 37.20% genotypes formed a superficial “Mixed/Admixture” subpopulation. All polymorphic SSR markers generated 36 alleles, averaging to 4.5 alleles/locus (2–7 range). The PIC and H were highest in MS31 and lowest in MS28, with averages of 0.66 and 0.71. MAF and mean genetic diversity were 0.16 and 89.28%, respectively. All these parameters indicated the presence of predominant genetic diversity and population structure amongst the studied genotypes. Based on AII, only 6 genotypes were found to be R. maidis resistant. SubPop3 had 91.66% (11) of the resistant or moderately resistant genotypes. SubPop3 also had the most pure genotypes (11), the least aphid infestation (8.78), and the highest GS (0.88), indicating its suitability for future R. maidis resistance breeding initiatives.

Construction of the core germplasm of yellowhorn (Xanthoceras sorbifolium Bunge) using physiological traits and SSR markers

Yellowhorn (Xanthoceras sorbifolium Bunge) is an important ecological, economic, and ornamental plant species native to China. However, the physiological diversity, genetic variation, and core germplasms have not been revealed, which hindered the breeding process of yellowhorn. Here, we evaluated the genetic diversity of 155 yellowhorn germplasms using five physiological traits. The content of flavonoids varied significantly in different germplasms, and it was positively correlated with soluble sugar content (P < 0.01). A total of 253, 336 candidate SSR were identified from the whole genome of yellowhorn. A moderate genetic diversity was found in yellowhorn based on the mean values of the number of effective alleles (Ne = 2.307), expected heterozygosity (He = 0.527), and observed heterozygosity (Ho = 0.317) with 30 pairs of polymorphic SSR markers. Population structure, Neighbor-Joining phylogeny, and principal coordinates analyses divided all genotypes into two major groups with few admixtures. Meanwhile, we extracted 34 (21.94 %) core yellowhorn germplasms based on the variation in physiological traits (14 germplasms) and genetic diversity (23 germplasms). After multiple different analyses including genetic diversity parameters, coincidence rate of range, variance difference percentage, and coefficient of variation rate of change, there was no obvious difference between core and original germplasm, which indicated that the core germplasm could represent the original germplasm well. Our study will lay a solid foundation for future conservation and management of yellowhorn germplasms and the core collection will be valuable in molecular breeding programs.

SSR marker based profiling and population structure analysis in peach (Prunus persica) germplasm

For breeding programmes to be successful and for germplasm conservation, it is essential to characterize and analyze the genetic diversity of available germplasm. The present experiment was conducted at Molecular Biology and Genetic Engineering Laboratory of Uttarakhand Council for Biotechnology, Haldi, Uttarakhand during 2022 to study the molecular profile of 41 peach [Prunus persica (L.) Stokes] accessions using 23 polymorphic SSR markers. The number of alleles detected ranged from 3 to 8 with an average of 4.65 alleles per locus (Na) and a total of 107 alleles were amplified. The average effective number of alleles (Ne) were 2.89 per marker. The SSR marker MA015a produced maximum number of 8 alleles followed by BPPCT 015 and CPPCT14 which produced 7 alleles each. The polymorphic information content (PIC) varied between 0.317–0.836 with a mean value of 0.563. The observed heterozygosity examined was lower (Ho = 0.02) and the expected heterozygosity (He = 0.61) ranged between 0.34 to 0.85. The presence of a higher Shannon’s information index (I) of 1.17 indicates higher diversity in the given set of peach genotypes. Jaccard’s similarity coefficient ranging from 0.533 to 1, indicated a pair-wise relationship among the peach accessions. The cluster dendrogram partitioned the accessions into two main clusters. However, the total accessions were stratified into 3 groups (K=3) based on population structure analysis which was further confirmed by Principal Coordinate Analysis (PCoA). The information generated in the study may have great implications in molecular characterization, fingerprinting and documentation of accessions in the peach improvement programme.

Genomics and Physiology of Chlorophyll Fluorescence Parameters in Hordeum vulgare L. under Drought and Salt Stresses.

To map the genomic regions and control chlorophyll fluorescence attributes under normal, salinity-, and drought-stress conditions in barley (Hordeum vulgare L.) at the seedling stage, an experiment was conducted in 2019-2020 using 106 F8 lines resulting from the cross between Badia × Kavir. Initially, the different chlorophyll fluorescence parameters were evaluated. Under drought stress, the highest decrease was related to REo/CSm (59.56%), and the highest increase was related to dV/dto (77.17%). Also, under salinity stress, the highest decrease was related to Fv/Fo (59.56%), and the highest increase was related to DIo/RC (77.17%). Linkage maps were prepared using 152 SSR polymorphic markers, 72 ISSR alleles, 7 IRAP alleles, 29 CAAT alleles, 27 Scot alleles, and 15 iPBS alleles. The obtained map accounted for 999.2 centi-Morgans (cM) of the barley genome length (92% of the whole barley genome). The results indicated the importance of chromosomes 3, 2, and 7 in controlling ABS/CSm, Area, ETo/CSm, Fm, Fv, and ETo/RC under drought stress. qEToRCD-7, as a major QTL, controlled 18.3% of ETo/RC phenotypic variation under drought stress. Under salinity stress, the regions of chromosomes 2 and 7 (102 cM and 126 cM) controlled the parameters ABS/CSo, Fm, Fo, Fv, TRo/SCo, Area, ETo/CSm, and ETo/CSo. The results showed that chlorophyll fluorescence is an important parameter in the study of drought and salinity effects on barley. This is the first report of the investigation of changes in the genetic structure of quantitative genes controlling the fluorescence parameters associated with barley response to drought and salinity stresses in the Iranian barley RILs population. According to the obtained results, it is possible to use HVPLASC1B and EBmac0713 in normal conditions, ISSR21-2 and ISSR30-4 in drought conditions, and Bmac0047, Scot5-B, CAAT6-C, and ISSR30iPBS2076-4 in saline stress conditions to select genotypes with higher photosynthetic capacity in marker-assisted selection programs.

Molecular characterization of bread wheat (Triticum aestivum) genotypes using SSR markers

An experiment was conducted during winter (rabi) seasons of 2019–20 and 2020–21 at the research farm of CCS Haryana Agricultural University to study the genetic diversity of 80 bread wheat (Triticum aestivum L.) genotypes, using 43 polymorphic SSR markers. A total of 84 alleles were discovered, with an average of 3 alleles amplified per locus. The average value of the allelic PIC varied from 0.26 to 0.82. Primers, viz. Xgwm 129, Xgwm 131, TaGST, CFA2147, Xwmc48, Xbarc 1165 and Xwmc169 may be deemed particularly informative given their high PIC values. Indices of dissimilarity varied from 0.14 to 0.42. Eighty wheat genotypes were clustered into two main groups with 35 and 45 genotypes each using the dendrogram constructed on the basis of molecular data of polymorphic markers. Using STRUCTURE, genotypes were classified into 4 major sub-populations having Fst values 0.351, 0.363, 0.508 and 0.313, respectively. Future breeding operations in wheat cultivars for tolerance to abiotic stress should consider genotypes clustering into different groups. Assessing the molecular genetic diversity is a reliable approach to identify cultivars by analyzing of specific regions of the cultivars DNA based on their unique genetic profiles.

Association mapping of total flavonoid content and antioxidant capacities in lentil (Lens culinaris Medik.)

Ninety-six lentil genotypes were characterized for total flavonoid content (TFC) and antioxidant capacities (AOC). Analysis of variance (ANOVA) indicated significant (p ≤0.01) differences among lentil genotypes for studied traits across three locations. The average content of TFC was relatively higher in advanced breeding lines (12.21 mg QE/g) and low in Indian germplasm lines (10.68 mg QE/g). Mean performances for AOC, using the DPPH (ACD) and CUPRAC(ACC) methods, were relatively higher in advanced breeding lines (ACD-4.32 μmolTE/g and ACC-1.25 μmolTE/100 g) and least in released varieties (ACD-2.79 μmolTE/g and ACC-0.92 μmolTE/100 g). Marker trait association analyses were performed with 87 polymorphic SSR markers. The number of alleles amplified per locus ranged from 2 to 5, with an average of 2.92. The polymorphism information content (PIC) value ranged from 0.04 to 0.67, with a mean of 0.25. SSR markers, LCSSR 363 and PLC 38 were significantly associated with TFC and explained 10% of phenotypic variation. PLC 60, SSR 80, PLC 77, and PBALC 216, associated with ACD, explained 7.5 to 23% of phenotypic variation, whereas PBALC 250 and PBALC 216, associated with ACC, explained 15% of the phenotypic variation. TFC and AOC have a broader range of genetic variations that can be used in lentil breeding programs to develop varieties tailored for nutraceutical and therapeutic applications. The identified markers can be validated in biparental populations and used in lentil breeding programs to improve functional constituents and health benefits.

Genetic studies and mapping of quantitative trait loci (QTL) for yield and yield-related traits in vegetable and seed soybean (Glycine max L.) -derived populations

Understanding the genetic control of seed yield and yield-related traits is essential for its targeted manipulation and genetic improvement. In this study, vegetable soybean (Glycine max L.) genotype- AGS457, and seed soybean genotype- SKAF148 derived F2 and F2:3 populations were phenotyped in the field for yield and yield-related traits and were genotyped with SSR markers for understanding genetic control and mapping of the yield and yield related traits. Normal frequency distribution of the traits indicated polygenic inheritance of yield and yield-related traits under study. The genetic map constructed with 105 polymorphic SSR markers covered 2005.7cM across 20 chromosomes of soybean. In the F2 generation of the crosses, 11 distinct QTLs were mapped for the yield and yield-related traits with any single QTL explaining 4.9 to 27.93% phenotypic variations of the trait concerned. The 11 QTLs were mapped on 9 different chromosomes viz., 5, 6, 7, 9, 11, 13, 16, 18 and 19. Similarly, 19 QTLs were mapped in the F2:3 population with phenotypic variation explained (PVE) by any single QTL ranging from 3.27 to 23.14%. The QTLs in the F2:3 population were mapped on 12 different chromosomes viz., 1, 3, 4, 6, 7, 10, 11, 12, 13, 16, 18 and 20. Three QTLs, one each for plant height at maturity (qPHM11-1), two-seeded pod length (qTSPL16-1) and seed weight per plant (qSWPP6-1) were consistent across F2 and F2:3 generations. Most of the 19 QTLs mapped in this study were novel ones. The knowledge of genetic control of the target traits and their mapping with SSR markers would facilitate the deployment of these QTLs for enhancing yield and other related traits in soybean.

ИССЛЕДОВАНИЕ ФЕНОТИПИЧЕСКИХ И ГЕНЕТИЧЕСКИХ ПРИЗНАКОВ ОТЕЧЕСТВЕННЫХ СОРТОВ ЧЕРЕШНИ

One of the tasks in the research of the gene pool of fruit crops is a systematic phenotypic assessment of samples in collections and the study of their genetic diversity. To date, traditional methods of varietal study and DNA marking are used for this purpose, which make it possible to identify donors and sources for breeding and promising varieties for industrial cultivation. The aim of the research was a comprehensive phenotypic and genotypic evaluation of varieties and hybrids of sweet cherries of domestic breeding. A long-term phenotypic assessment, carried out against the background of unstable and stressful conditions of the growing year, made it possible to identify more plastic varieties of sweet cherries Kavkazskaya uluchshennaya, Kavkazskaya, Podarok leta, combining the signs of winter hardiness, drought resistance, resistance to coccomycosis, and productivity. Simultaneous assessment of sweet cherry varieties of local breeding based on the analysis of polymorphism of microsatellite loci made it possible to establish genetic characteristics and perform DNA certification. To analyze the polymorphism of the studied genotypes, we used 7 SSR loci that were first identified and mapped in the sweet cherry genome (Alaya, Madonna, Kavkazskaya, Kavkazskaya uluchshennaya, Krasna devitsa, Mak, Podarok leta, Yasno solnyshko, Luchezarnaya, Yuzhnaya). Analysis of the obtained DNA fingerprints made it possible to establish that all the studied varieties of sweet cherries have a unique allelic set. For DNA certification of cherry varieties, the most polymorphic SSR markers are recommended: EMPa018, EMPaS12, EMPa017, EMPa004, UCDCH17, UCDCH12 and UCDCH31. Sweet cherry varieties Madonna (early), Podarok leta (middle) and Alaya (late) have been identified as sources of a complex of adaptive and productive traits recommended for further breeding work, as well as varieties that are for laying new cherry plantations in the south of the country.

Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in Fagopyrum esculentum and Fagopyrum tataricum.

Characterisation of genetic diversity is critical to adequately exploit the potential of germplasm collections and identify important traits for breeding programs and sustainable crop improvement. Here, we characterised the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species Fagopyrum esculentum and Fagopyrum tataricum (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers. A wide range of variation was observed in both species for most of the traits analysed. The two species differed significantly in most traits, with traits related to seeds and flowering contributing most to differentiation. The accessions of each species were divided into three major phenoclusters with no clear geographic clustering. At the molecular level, the polymorphic SSR markers were highly informative, with an average polymorphic information content (PIC) of over 0.65 in both species. Genetic diversity, as determined by Nei's expected heterozygosity (He), was high (He = 0.77 and He = 0.66, respectively) and differed significantly between species (p = 0.03) but was homogeneously distributed between regions, confirming the lack of genetic structure as determined by clustering approaches. The weak genetic structure revealed by the phenotypic and SSR data and the low fixation indices in both species suggested frequent seed exchange and extensive cultivation and selection. In addition, 93 and 140 significant (p < 0.05) marker-trait associations (MTAs) were identified in both species using a general linear model and a mixed linear model, most of which explained >20% of the phenotypic variation in associated traits. Core collections of 23 and 13 phenotypically and genetically diverse accessions, respectively, were developed for F. esculentum and F. tataricum. Overall, the data analysed provided deep insights into the agro-morphological and genetic diversity and genetic relationships among F. esculentum and F. tataricum accessions and pointed to future directions for genomics-based breeding programs and germplasm management.

Pyramiding resistance genes for bacterial leaf blight (Xanthomonas oryzae pv. Oryzae) into the popular rice variety, Pratikshya through marker assisted backcrossing.

Bacterial leaf blight (BLB) is one of the major biotic stress in rice cultivation. Management techniques, such as the development of BLB-resistant cultivars, are required to lessen the severity of the disease attack and yield losses. Pratikshya was selected in the present investigation as the recipient parent, as it is one of the popular high-yielding rice varieties of Odisha, India, which is having excellent grain as well as cooking quality. However, Pratikshya is highly susceptible to BLB which is prevalent in Eastern Indian region. Three major BLB resistance genes xa5, xa13, and Xa21 from the donor source Swarna MAS (CR Dhan 800) were attempted to introduce into Pratikshya through a marker-assisted backcross breeding program. Those markers closely linked to the target genes were employed for foreground selection in the segregating generations till BC2F3. In each backcross generation, progenies containing all three targeted resistance genes and phenotypically more similar to the recipient parent, Pratikshya were selected and backcrossed. Screening of 1,598 plants of the BC2F2 population was conducted against BLB using Xoo inoculum and 35 resistant plants similar to Pratikshya were carried forward to the next generation. In the BC2F3 generation, 31 plants were found to possess all the three resistance genes. For background selection of plants carrying resistance genes 45 polymorphic SSR markers were employed. Evaluation of the pyramided lines at BC2F4 generation exhibited that, most pyramided lines were similar to Pratikshya in terms of morphological features and yield parameters, and some lines were superior to the recurrent parent in terms of morphological features and yield parameters. The three-gene pyramided lines showed a high level of resistance to BLB infection and are anticipated to offer a significant yield advantage over the recipient parent Pratikshya.The pyramided lines can further be used for multi-location trial, so as to be released as a variety or can be used as a potential donor for BLB resistance genes.

SSR Markers are Useful Tools in Wheat Varietal Purity and Genetic Diversity Assessment

Assessing genetic similarity and purity degree among wheat cultivars is important in breeding programmes and SSR markers have all the features that make them suitable for this purpose. The aim of this study was to assess the varietal purity and genetic diversity among wheat cultivars grown in Romania using 22 SSR markers and to choose the most informative markers. The 40 samples included in the study consisted of seeds from certified and non-certified wheat cultivars, and from other related species. To establish that varietal purity is maintained, seeds from 14 certified wheat cultivars were analysed from two harvesting campaigns (years 2019 and 2020) and seeds of four of them were also compared with the authors' seeds. The most polymorphic SSR marker was Xwmc596 (seven alleles), followed by Xwmc603 and Xwmc474 (six); Xgwm71, Xbarc347 and Xbarc074 (five); Xgwm469, DuPw004, Xgwm155 and Xbarc184 (four); Xwmc418, Xbarc170, Xwmc533, DuPw167, DuPw115, Xgwm413 and Xgwm372 (three); and DuPw217, DuPw205, Xgwm003 and Xgwm095 (two). SSR marker Xgwm052 showed low polymorphism (one). No contamination of the varieties was observed in these harvesting campaigns since all SSRs markers showed high similarity in the certified wheat cultivars harvest analysis; genetic diversity between genotypes was also observed.

Genome-wide microsatellite characterization and marker development in Diospyros oleifera

Diospyros oleifera, a diploid Diospyros, have a wide range of applications in biomedical science and the food, wood, and chemical industries. In addition, it is an excellent model plant to study Diospyros. While, to date, the genome-wide mining of SSRs (or Microsatellite) in D. oleifera is still absent. In this study, we constituted the first deep characterization of genome-wide microsatellites for D. oleifera and developed polymorphic SSR markers across Diospyros lotus and Diospyros kaki. A total of 330,507 SSRs were identified from D. oleifera genome with an average density of 385.95 SSRs per Mb, representing a higher SSR density. D. oleifera SSR motifs are not randomly distributed across genomic regions and motif types. Although, the distribution of SSRs differed slightly among D. oleifera chromosomes, only chromosomes 1 and 5 had considerably high densities. There are significantly lower frequencies of SSRs in the coding regions than that in the whole genomic region, which was only about 3.49% of the density of the D. oleifera genome (13.48/Mb vs. 385.95/Mb). Of the different SSR motif types, mononucleotide repeats (47.63%) were the most abundant in genome, while trinucleotide repeats (68.57%; 1924) were the most abundant in coding regions. Therefore, unlike in the D. oleifera genome, the AT-rich motif lost its numerical dominance in the coding regions. In addition, 231,809 primer pairs were identified, and 87.65% were high-resolution markers in the D. oleifera genome, which generated no more than three in silico products. 25,387 potential for interspecific polymorphic SSR markers between two Diospyros species were also identified. An amplification rate of 92% from testing Diospyros species were clarified through with a subset of candidate polymorphic markers (100 markers) test. Then, 29 novel polymorphism SSR markers were employed to distinguish among 12 Diospyros accessions with high mean PIC values of 0.6009. Thus, these SSR locus we identified in this study had the potential to reveal genotypic diversity in Diospyros.

Genetic diversity analysis in sunflower (Helianthus annuus L.) restorer lines using SSR markers

Sunflower is a staple oilseed crop ofthe world. Genetic diversity in the parental lines is key for hybrid breeding programmes in sunflower. In this study, genetic diversity in a set of 102 parental lines (100 restorer and twoCMS) of sunflower was assessed using 69 polymorphic SSR markers. The genetic diversity parameters: average number of alleles (3.07) per locus, gene diversity (0.356) and polymorphism information content (0.296) revealed low to moderate genetic diversity in the restorer lines. The SSR marker ORS447 located on linkage group 2 was more informative with high number of alleles (10) and high PIC value (0.89). Cluster analysis (neighbour-joining tree) revealed three major genotypic groups. Model based STRUCTURE analysis showed recognizable population structure; based on membership coefficients(&gt;80%), 82 genotypes were classified into two populations (K=2) and the remaining 20 genotypes were classified into admixture group. The Fst value (0.278) suggested that the populations were differentiated. Analysis of molecular variance resultsshowed that maximum of genetic variation (72%) was observed between the individuals within the population suggesting that the population was weakly structured. These results would be useful for selecting SSR markers for genotype characterization as well as choosing diverse parents for hybrid development programme in sunflower.

Transfer of Stress Resilient QTLs and Panicle Traits into the Rice Variety, Reeta through Classical and Marker-Assisted Breeding Approaches.

Reeta is a popular late-maturing high-yielding rice variety recommended for cultivation in the eastern Indian states. The cultivar is highly sensitive to submergence stress. Phosphorus deficiency is an additional constraint for realizing high yield. The quantitative trait loci (QTLs), Sub1, for submergence and Pup1 for low phosphorus stress tolerance along with narrow-grained trait, GW5 were introgressed into the variety from the donor parent, Swarna-Sub1 through marker-assisted breeding. In addition, phenotypic selections for higher panicle weight, grain number, and spikelet fertility were performed in each segregating generation. Foreground selection detected the 3 target QTLs in 9, 8 and 7 progenies in the BC1F1, BC2F1, and BC3F1 generation, respectively. Recurrent parent's genome recovery was analyzed using 168 SSR polymorphic markers. The foreground analysis in 452 BC3F2 progenies showed five pyramided lines in homozygous condition for the target QTLs. No donor fragment drag was noticed in the Sub1 and GW5 QTLs carrier while a segmentwas observed in the Pup1 carrier chromosome. The developed lines were higher yielding, had submergence, and had low phosphorus stress-tolerance alongwith similar to the recipient parent in the studied morpho-quality traits. A promising pyramided line is released in the name of Reeta-Panidhan (CR Dhan 413) for the flood-prone areas of Odisha state.

Physiological and Molecular Screening of High Temperature Tolerance in Okra [Abelmoschus esculentus (L.) Moench

Okra is a vegetable crop adapted to summer temperatures, but heat stress has been shown to reduce its growth and productivity. We measured physiological traits of 104 okra genotypes in response to high temperature, augmented by the molecular characterization of selected genotypes to identify parents for crossing. Genotypes were exposed to a short heat shock (45 °C, 4 h) in a controlled environment, followed by the assessment of chlorophyll fluorescence (Fv/Fm, Fv′/Fm′) and stomatal conductance (gs). DNA was isolated from all genotypes using a modified CTAB method with additional PVP and RNase, and the amplification of 8 polymorphic SSR markers was used to generate a dendrogram. This preliminary screening identified 33 polymorphic genotypes with less than 50% genetic similarity and contrasting Fv′/Fm′ and gs responses. More detailed physiological measurements (Fv/FmFv′/Fm′, gs, photosynthesis (A), efficiency of the open reaction centre (ΦPSII), and electrolyte leakage (EL)) were conducted after exposure to 45 °C for 6 h and compared to the control (30 °C). EL did not significantly increase in the heat treatment; in contrast, there were significant genotype and treatment effects observed for fluorescence (Fv/Fm, Fv′/Fm′) and photosynthetic parameters (A, ΦPSII, gs). In conclusion, cell membranes in okra remained unaffected after short periods of heat stress, whereas the ranking of differences of measured physiological traits (∆) between control and heat-treated plants (∆Fv′/Fm′, ∆Fv′/Fm′, ∆A, ∆ΦPSII, ∆gs) was indicative of genotype sensitivity to heat.

SSR and 18S rDNA based molecular profiling of Neopyropia yezoensis (Rhodophyta) in China: insight into genetic impact of laver aquaculture on wild resource

Neopyropia yezoensis is a typical intertidal seaweed and an indispensable species for conservation of seaweed resources. As one of the most important marine vegetables, the cultivation area of N. yezoensis has been largely increasing in the past decade and ranked the second highest among all the farmed seaweeds in China. It remains unknown whether large-scale cultivation of N. yezoensis has a genetic impact on wild populations. In this study, SSR markers and 18S rDNA were applied for diversity and genetic structure analysis of 22 N. yezoensis populations from North China. Twenty-two haplotypes were generated from 352 18S rDNA sequences and only three haplotypes were shared by both cultivated and wild populations. Based on 11 polymorphic SSR markers developed, the average polymorphism of the cultivated N. yezoensis populations was higher than that of the wild populations, with the percentage of polymorphic loci being 90.91% in most cultivated populations. The cultivated populations were clustered separately from the wild ones based on the population phylogenetic tree. This indicates that cultivated N. yezoensis populations are diverse and divergent from wild populations in China. However, there were cultivated individuals mixed with the wild ones based on the individual phylogenetic tree and STRUCTURE analysis. The genetic differentiation between cultivated and wild populations decreased with increasing cultivation time, suggesting a possible long-term and slow process of genetic introgression between cultivated N. yezoensis and the wild resource. The wild populations were grouped into two distinct clades by SSRs, with one distributed around the intersection between the Yellow Sea and the Bohai Sea, where the populations were characterized by a specific 18S rDNA haplotype. These findings provide useful insights into germplasm conservation, genetic breeding and improvement of N. yezoensis farming practices.