Highest Polymorphism Information Content Value Research Articles

The genetic diversity and population structure of wild and cultivated Avena species in Ethiopia using a SSR markers

Oats are grains that can be consumed by both animals and humans. They have thrived in Ethiopia, where certain oat species are considered native to the region. This work represents the first investigation of the population structure and genetic diversity of Ethiopian and other country oats. This led the scientists to explore the genetic diversity and population structure of wild and cultivated Ethiopian oats (Avena) species as well as oat cultivated in USA, the Netherlands and Austria. This study's main objective looks to be to investigate the variation in genetic makeup of cultivated and wild oat species. Studying the population structure of the oat species in the germplasm of Ethiopia, USA, the Netherlands and Austria. We used nineteen fluorescent SSR (simple sequence repeat) markers since previous research had indicated that these markers had high PIC (polymorphism information content) values. Five species of Avena were studied among the 176 oat accessions: A. sativa (cultivated oats) and four wild oats, such as A. abyssinica, A. vaviloviana, A. fatua, and A. sterilis. The AMOVA investigation revealed significant genetic distinctions among populations, individuals, and within individuals, explaining 18 % of the variance within populations, 4 % among populations, and 78 % within individuals. The AMOVA analysis of Avena species demonstrated extensive variance, with 33 % variation among species and 67 % within each species, underscoring robust species differentiation. The study also discovered gene interchange between wild oat and cultivated populations, defining two Avena species: domesticated oats and wild oats. Using the STRUCTURE software at K = 2, PCoA, and UPGMA, a distinct genetic structure was displayed in the dataset. Despite variations in ploidy levels and genomes, A. sterilis and A. vaviloviana were determined to be more closely linked, whereas A. abyssinica and A. fatua demonstrated a close association. This research delivers valuable insights for scientists and can be employed in oat breeding programs to improve future oat yield and productivity.

Molecular diversiry studies among blackgram genotypes for yellow mosaic virus resistance

Yellow mosaic disease (YMD), incited by a geminivirus. Mungbean Yellow Mosaic Virus (MYMV), is transmitted by whiteflies, poses a significant threat to various leguminous crops in India. This study focuses on identifying resistant sources and validating molecular markers for their efficacy in detecting YMV resistance in blackgram. In the present study, 150 blackgram genotypes were evaluated to identify resistant sources for YMD under natural field conditions and through molecular markers. Among the 150 genotypes, 22 (both resistant and susceptible) were selected based on field screening. These genotypes were validated using 15 molecular markers, including 8 simple sequence repeats (SSRs) and 7 gene-specific markers linked to MYMV resistance. The markers amplified a total of 48 alleles, with polymorphic information content (PIC) values ranging from 0.82 (CEDG67) to 0.21 (HSP), with an average value of 0.55. The highest PIC values were exhibited by markers CEDG67 (0.82), CEDG115 (0.81), and CEDG20 (0.74). Cluster analysis using DARWIN revealed that most phenotypically resistant genotypes grouped together, while susceptible genotypes formed separate clusters. The genotypes LBG 904, LBG 932, LBG 884, PU 1815, PU 1808, PU 1803, MASH 1008, MASH 114, VBN 10, and PU 31 exhibited resistance to YMV phenotypically. Among these, LBG 904, LBG 932, PU 1815, PU 31, and MASH 1008 produced a 162 bp resistant allele using the marker CEDG180. Similarly, the gene-specific marker DEF produced a 190 bp resistant allele in all the resistant genotypes, whereas the susceptible genotypes produced both 190 and 250 bp alleles. These identified genotypes can serve as valuable sources for MYMV resistance in blackgram breeding programs. Keywords: SSR markers, Blackgram, Diversity, MYMV

Individual Identification and Assessment of Genetic Diversity Using Microsatellite Markers in Racing Pigeons Raised in Turkiye

The implementation of a swift and economical molecular genetic approach, ensuring both efficacy and cost-effectiveness and facilitating population certification, is of utmost significance for breeders and the conservation of Turkiye's native pigeon biodiversity. In this study, we aimed to examine the genetic structure of racing pigeons (Columba livia domestica) raised in Turkiye using a genetic marker panel consisting of eight short tandem repeat (STR) loci. For this purpose, DNA was isolated from the shed feathers of 216 pigeons. Genomic DNA was amplified using the multiplex allele-specific PCR and subsequent capillary electrophoresis with ABI PRISM 3130XL Genetic Analyzer. Next, PCR products were analyzed in the GeneMapper Software program (Applied Biosystems). For parent testing, paternity index (PI), combined paternity index (CPI), and cumulative probability of paternity (CPP) were calculated. Furthermore, population genetic diversity was evaluated using heterozygosity (He), polymorphism information content (PIC), and Hardy–Weinberg equilibrium (HWE) testing. Results revealed that the total number of alleles is 81 and the number of alleles per locus varies between 4 and 19. The similarity rate between parent and offspring was calculated as 99.99% and above. Since no pedigree information was given when the samples were analyzed, obtaining this similarity ratio demonstrates the reliability of the panel. He values range from 0.362 to 0.919, and the PIC values range from 0.295 to 0.909. Loci PG-1, PG-2, and PG-3 show significant genetic diversity, with moderate to high PIC values reflecting varied allele frequencies in the population. Consequently, the set of seven STR markers (+ one sex marker) can be applied to identify and confirm parentage on a regular basis, thereby facilitating efficient breeding programs and ensuring genetic diversity conservation. This panel enables efficient pedigree analysis and gender determination, optimizing cost-effectiveness. The methodology presented in this study is ideal for pedigree analysis and breed certification in the Turkish pigeon breeding industry. Consequently, we affirm that the study data carries considerable national importance.

Phenotypic and Molecular-Markers-Based Assessment of Jamun (Syzygium cumini) Genotypes from Pakistan

Jamun plant displays enormous diversity throughout Pakistan, which necessitates its screening, evaluation, and validation to document elite genotypes having better traits for the benefit of the fruit industry and farmers. Surveys were made in natural Jamun habitats across Punjab, Pakistan, and genotypes were marked based on visual diversity of trees and fruits. In total, 60 Jamun genotypes were selected for characterization based on phenotypic and genetic markers. Phenotypic characters related to trees, leaf, and flower along with fruit qualitative traits were assessed in situ. Results revealed significant diversity with high (>25%) coefficient of variance values and the first two components of correspondence analysis exhibited 41.71% variation among genotypes. A strong association was observed among traits like upright tree and round fruit shape (0.74), bluish-colored fruit and pinkish pulp (0.85), and elliptic-shaped fruit with low fruit waxiness (−0.72). Leaves of phenotypically characterized plants were brought to Wheat Biotechnology Lab., University of Agriculture, Faisalabad, Pakistan, where Jamun genotypes were investigated genetically using Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) markers. A total of 132 bands were scored, of which 108 were polymorphic, corresponding to almost 81% polymorphism among collected genotypes. High polymorphism information content values were observed against RAPD (0.389) and ISSR (0.457) markers. Genotypes were compared in relation to genetic markers, which exhibited that almost 86% of genetic variability was attributed to differences among accessions, while 14% of variation was due to differences between collections of different areas. Findings of this study confirmed wide phenotypic and genetic distinctness of Jamun in Pakistan that can aid breeders for marker-assisted selection and germplasm enhancement for future crop improvement programs.

Molecular characterization of Turkish hazelnut cultivars and genotypes using SSR markers

This study defines the genetic characterization of 16 hazelnut varieties and 64 genotypes. SSR method was used in molecular characterization studies. 18 SSR primers were used. In the SSR method, 118 bands were obtained, and 115 were polymorphic. The similarity coefficient in overall genotypes were between 0.12 and 0.98 in SSR andthe polymorphism rate of the primer pairs used was calculated as 98.0%. The lowest polymorphism information content value (0.542) was obtained from the CAC- C 028 locus, and the highest polymorphism information content value (0.987) was obtained from the CAC- B 113 locus. The average polymorphism information content value was 0.786. The total discrimination power values of SSR loci were determined as 17.98; the lowest (0.748) discrimination power value was obtained from the CAC- B 020 locus, while the highest (1.404) discrimination power value was obtained from the CAC- A 024 b locus. The genotypes’clustering positions across the dendograms were essentially correlated with their geographic origins. This result shows that genetic origin plays an important role in terms of classification of genotypes in hazelnut.

Genetic diversity of maize resources revealed by different molecular markers

AbstractMaize (Zea mays L.) is the third most important cereal crop in the world because of its nutritional value and industrial benefits. Molecular markers are used mainly by the breeders to study the genetic variability of genotypes and its application in the breeding process. Two types of molecular markers, 10 random amplified polymorphic DNA (RAPD) primers and 10 start codon target (SCoT) primers, were assayed to determine the genetic diversity of 25 Slovak maize lines and 25 maize cultivars. A high level of polymorphism was found with both RAPD and SCoT markers, which was confirmed by high average polymorphism information content (PIC) values using both techniques. The efficiency of individual marker techniques in the detection of genotype diversity can be compared by calculating the marker index (MI), detecting diversity index (DDI), discriminating power, resolving power (RP) and other indices. A higher MI (11.788), DDI (2.358) and RP (53.08) value was achieved by the SCoT technique compared to the RAPD method. Three joint dendrograms and PCoA plots constructed based on RAPD, SCoT and both methods combined confirmed the unambiguous separation of maize lines and cultivars from each other. The results obtained from the RAPD and SCoT analysis can be used for the selection of potentially suitable biological sources for further marker-assisted breeding.

Genetic Relatedness in Elite Cultivars of Moth Bean using Morpho-agronomic and Molecular Markers

Background: Moth bean is a very nutritive and hardy crop, especially for resource poor-arid agriculture. The limited use of cultivars in moth bean breeding resulted into narrow genetic base. This study aimed to diversify the conical genetic base and developimproved cultivars, through molecular (RAPD) and morpho-agronomic characterization of commercially elite moth bean cultivars. Methods: Elite moth bean cultivars (15) were evaluated for 11 morpho-agronomic traits. Eleven RAPD markers were used to amplify genomic DNA and perform molecular characterization.Clustering approach was used for grouping of the cultivars. Result: RAPD markers revealed high polymorphism in 15 elite moth bean cultivars. The polymorphism information content (PIC) values varied within the range of 0.45 to 0.88, with an average of 0.77. The number of alleles at different loci ranged from 4 to 16, with an average of 10 alleles per locus. When employing UPGMA-based cluster analysis, utilizing 11 morpho-agronomic traits, the cultivars were grouped into four clusters. However, when RAPD markers were used, the cultivars were grouped into five clusters. The Jaccard’s similarity coefficient and Manhattan dissimilarity coefficient fell within the ranges of 0.18 to 0.70 and 0.02 to 0.42, respectively. These values signify the degree of genetic variability within the cultivars. Furthermore, a Mantel test was conducted to examine the correlation between agronomic traits and the RAPD-based matrix. The results showed a negative correlation, but it was not statistically significant.The high PIC values and the successful amplification of multiple loci demonstrate the efficacy of RAPD markers in assessing genetic diversity in moth beans. The study revealed enormous genetic variation among cultivars and crosses can be attempted between cultivars of different groups to create better recombinants in moth bean breeding programmes.

Genetic diversity and population structure of Anatolian Hair goats, an ancient breed

Abstract. This study aimed to investigate the genetic characterization and diversity of Hair goats from 10 regions using 20 microsatellite markers. A total of 522 alleles were observed. The INRA0023 locus exhibited the greatest number of alleles (48), while the DRBP1 locus had the highest effective allele number (16.27), and the BM1818 and DRBP1 loci had the highest polymorphic information content value (0.94). The expected heterozygosity value ranged from 0.85 (ILSTS011) to 0.94 (BM1818, SRCRSP15, and DRBP1). The Hair goat populations in Konya and Hatay displayed the lowest and highest allele numbers, with values of 10.40 and 16.25, respectively. The fixation index (FIS) values are significant in defining population structures and determining the extent of heterozygosity losses. The FIS values exhibited a range of 0.031 in Muǧla to 0.226 in Burdur. A total of 107 unique alleles were identified in Hair goat populations. However, it is noteworthy that, out of all the alleles, only 25 had a frequency exceeding 5 %. The results indicate that the microsatellite markers utilized demonstrate sufficient levels of polymorphism, making them appropriate for efficiently investigating the genetic variability of Hair goat populations.

Microsatellite-Based Genetic Diversity Analysis and Population Structure of Proso Millet (Panicum miliaceum L.) in Kazakhstan

Proso millet is an important allotetraploid cereal crop; however, it is the least studied species of the Poaceae family, as it is an under-utilized crop. Genomic resources for proso millet are very limited compared to major crops. An understanding of the genetic relationships among germplasm resources is important for future breeding endeavors. In the present study, simplesequence repeat (SSR) markers were employed to assess the polymorphism and genetic diversity of 100 millet accessions from different countries, which were tested in the dry steppe zone conditions of the Akmola region from 2020 to 2022. The use of 20 SSR markers detected a total of 47 alleles, with an average allele number of 2.35 per locus among these proso accessions. Nine of them were polymorphic among the genotypes, which suggests that these SSR markers can be used for genetic studies. The results showed a moderate level of polymorphism information content (PIC) that averaged at 0.424, ranging from 0.125 to 0.795. The markers SSR-67, SSR-82, SSR-85 and SSR-109 showed high PIC values of 0.536, 0.756, 0.795 and 0.758, respectively. Markers SSR 85 and SSR 86 significantly correlated to agronomic traits, such as productive tillering (PT) and grain yield (GY). The genetic structure, UPGMA cluster and PCoA assay indicated that the accessions that originated from Central Asia had higher genetic diversity. Based on structure (K = 3), all the accessions were divided into three groups, where the gene pool that originated from Central Asia wasdetected in all three clusters. Based on a principal component analysis (PCA), the accessions of Central Asian origin were genetically closer to the North Asian group.

Assessment of Genetic Diversity and Protein Content of Scandinavian Peas (Pisum sativum)

We produced homogeneous lines of 227 pea accessions from the Nordic Genetic Resource Center via single seed descent. The genetic diversity among these, mostly Scandinavian accessions, was investigated using three microsatellite markers, A9, AC58 and AA5. The microsatellites were highly informative and separated 153 of 194 accessions on a Neighbor Joining topology. The high polymorphism information content (PIC) values between 0.87 and 0.91 indicated that the gene bank material contains a large number of pea accessions with different breeding histories. The peas were grown in the field for two years and seed protein content showed variation between 9.3% and 34.1% over the years and accessions, respectively. The mean thousand seed weight was 152.05 g. More than 10 accessions had a protein content above 28%, showing that the collection has potential as breeding nursery for high-protein pea cultivars.

Efficiency of RAPD and SCoT Markers in the Genetic Diversity Assessment of the Common Bean.

Knowledge about the genetic diversity of the available common bean germplasm can help breeders properly direct the choice of genetic material in the breeding process. The aim of the present work was to estimate the usefulness of 10 RAPD and 10 SCoT markers in genetic diversity detection among 33 common bean genotypes. Both molecular marker systems were able to generate high levels of polymorphism in the genetic material, which was supported by the relatively high polymorphic information content (PIC) values observed for the used markers. The Diversity Detection Index (DDI) and Marker Index (MI) were used to compare the effectiveness of RAPD and SCoT markers. For both techniques, high values of MI and DDI were calculated, representing their effectivity. The SCoT markers showed higher values of the parameters used (MI = 7.474, DI = 2.265) than the RAPD markers (MI = 5.323, DDI = 1.612), indicating their higher efficiency in the detection of molecular variability. Three constructed dendrograms and PCoA plots were created using RAPD and SCoT, and both methods combined confirmed sufficient separation of the bean genotypes from each other. At the same time, a higher efficiency of SCoT markers compared to RAPD markers in the detection of the genetic diversity of beans was also proven. The results may be of future interest in the choice of genetically distant material for breeding purposes.

GENETIC PURITY AND DIVERSITY ASSESSMENT OF PARENTAL CORN INBRED LINES USING SSR MARKERS FOR PHILIPPINE HYBRID BREEDING

Accurate data and relevant insights on parental corn inbred lines' and hybrids’ genetic purity and diversity are essential for hybrid development and seed production. Here, the genetic purity and diversity of 19 parental yellow corn inbred lines were assessed using SSR markers. A total of 91 SSR markers were utilized, of which 61 were highly polymorphic and had high polymorphism information content value (PIC = 0.379). Genetic purity and diversity parameters were calculated from the generated SSR marker data. Observed pairwise genetic distances ranging from 0.257 to 0.808 implied high genetic dissimilarities among the accessions. Cluster analysis separated the parental lines into three distinct subclusters, which can potentially be a basis for generating heterotic groupings among the parental lines. Eight (8) out of the 19 parental lines showed considerable residual heterozygosity of ≤10%. Inbred line CML 431 displayed complete homozygosity across all 61 SSR markers. Inbred lines that have residual heterozygosity of >15% need purification through further breeding and selection. Out of the resultant F1 hybrids analyzed, only four (4) showed genetic impurity of ≤10%. It may be attributed to the intrinsic genetic impurity of parental line CML 452 (21.67%). In contrast, hybrids generated from two genetically pure parents (e.g., CML 431 and CML 575) showed low to no off-types. Overall, genetic purity and diversity determination of promising parental lines can be valuable for future yellow corn breeding programs in the Philippines.

Assessment of Genetic Diversity of Local Coffee Populations in Southwestern Saudi Arabia Using SRAP Markers

Coffea arabica, a member of the Rubiaceae family, is the most commercially important species of the genus Coffea. It has been grown on the mountain terraces of southwestern Saudi Arabia for centuries. At present, the species is subject to increased genetic erosion due to the abandonment of many gardens by their owners and the increasingly dry climate. The current study was carried out to determine the genetic diversity of 56 local coffee accessions collected from the southern regions of Saudi Arabia using 30 sequence-related amplified polymorphism (SRAP) markers. Six SRAP markers showed polymorphism among the 56 accessions. A total of 1125 bands, with an average of 187.5, was produced from all six SRAP primers. The polymorphic information content (PIC) ranged from 74.8 to 97.7, with an average of 91.4 for all studied SRAP markers. The high polymorphism percentage seen in this study, along with the high number of alleles produced and the high PIC values of the primers used, demonstrate that the SRAP approach was an effective molecular technique for assessing genetic diversity in the studied populations. The structural analysis showed a sharp peak, with no ambiguity, demonstrating the highest delta K value at K = 3 and K = 6, and the coffee accessions could be grouped into three and six main populations, respectively. The PCoA, cluster analysis, and structural population analysis results suggest considerable genetic diversity among coffee populations growing on the southwestern mountain terraces of Saudi Arabia. The 56 accessions were segregated into five groups, mostly according to geographic distribution. The accessions from the southern districts of Jazan region mostly clustered in groups 2 and 4, while the accessions from the northern districts of Al-Baha and Assir regions formed separate groups. Based on these analyses, accessions KSA1R, KSA6R, KSA21, KSA25, KSA37, KSA38, KSA42, KSA59, KSA60, KSA62, and KSA63 were the most divergent. The genotypes should be conserved for use in coffee-breeding programs to improve the agronomic value of the crop, broaden the genetic base of C. arabica in Saudi Arabia and increase environmental resilience. Additional molecular and functional genomics studies are necessary to further elucidate how this germplasm has evolved and enhance the value of local Arabica coffee diversity in the Kingdom.

Molecular Characterization of Different Soybean [Glycine max (L). Merril] genotypes by RAPD Markers

The present investigation was carried out on molecular characterization of different soybean genotypes by using RAPD markers. Genetic diversity of 10 soybean genotypes was studied using Random Amplified polymorphic DNA (RAPD). 12 RAPD primers were used for screening 10 soybean genotypes from which total 334 fragments were amplified. It was observed that 41.10% bands were polymorphic and 58.88% were monomorphic. The percent of polymorphic amplicons in banding pattern was calculated and it was highest in OPA-01 (67.85%) followed by OPA-11 (66.66%). Polymorphism information content (PIC) was calculated and highest PIC value was observed in OPA-01 (0.26) and lowest was observed in OPA-08 and OPA-05 (0.03). Maximum amplicons were produced in OPA-01 (56) and minimum in OPA-08 (11). Genetic relationship between soybean genotypes was determined on the basis of Jaccard’s pair wise similarity coefficient values and dendrogram was generated by UPGMA (Unweighted Pair Group Method with Arithmetic Mean) cluster analysis using dice’s similarity matrix through NT-SYS pc software. The dendrogram of RAPD analysis shows 8 clusters and sub clusters were revealed. The value of similarity coefficient ranged from 0.19 to 0.71. The maximum similarity percentage i.e. 71% was found between KDS-726 and KDS-922 genotypes. The minimum similarity i.e. 19% was found between IVT-33 and IVT-13. According to this information it is concluded that the KDS-726 and KDS-922 genotypes showed minimum genetic diversity as compare to the IVT-33 and IVT-13 genotypes. Therefore, understanding the genetic diversity of soybean genotypes is essential to broaden the genetic base and to further utilize in the MAS breeding program.

Genetic Diversity and Population Structure of Normal Maize Germplasm Collected in South Sudan Revealed by SSR Markers.

Maize is one of the leading global cereals, and in South Sudan maize cultivation occurs in nearly all of the country’s agro-ecological zones. Despite its widespread cultivation, farmers in South Sudan depend on undeveloped varieties, which results in very low yields in the field. In the current study, 27 simple sequence repeat (SSR) markers were used to investigate genetic diversity and population structures among 37 landrace maize accessions collected from farmers’ fields in South Sudan. In total, 200 alleles were revealed with an average of 7.4 alleles per locus and a range from 3.0 to 13.0 alleles per locus. The observed heterozygosity values ranged from 0.06 to 0.91 with an average of 0.35. High polymorphic information content (PIC) values were identified with a mean of 0.69, which indicates the informativeness of the chosen SSR loci. Genetic structure analysis revealed a moderate genetic differentiation among the maize populations with a fixation index of 0.16, while there was very high genetic differentiation within the groups of populations of three regions with a mean fixation index (F) of 0.37. An unweighted pair group method with an arithmetic mean (UPGMA) dendrogram clustered the 37 maize accessions into three groups with 43% genetic similarity. The clustering pattern of the maize accessions was moderately consistent with their collection area. The findings of this study will provide maize breeders with a better understanding of maize diversification as well as a reserve of genetic resources for use in the selection of advantageous and useful resources for the development of maize varieties in South Sudan.

Molecular Characterization of Land Races of Rice by Using SSR Markers (Oryza sativa L.)

The study was conducted to use thirty one rice land races for characterized the genetic diversity analysis at Seed Unit, UAHS, Shivamogga. The SSR markers (25 SSR markers) were used for the assessment of genetic diversity and relatedness among 31 rice landraces and all of them were found polymorphic. Twenty five SSR markers revealed 50 alleles in the 31 land races, the number of alleles per locus with an average of 2 per locus. Major allele frequency ranged from 0.58 (RM 25) to 0.94 (RM 229) with an average of 0.74 per marker. The PIC (polymorphism information content) value ranged from 0.12 (RM 229) to 0.66 (RM 481 and RM 25) with an average of 0.36 per marker. The PIC value of each marker, which was evaluated on the basis of its alleles, varied greatly all tested SSR loci-from 0.58 to 0.94 with an average of 0.74. The highest PIC value 0.49 was obtained for RM481 and RM25, followed by RM443 (0.47), RM224 (0.46) RM 159, RM 1054, RM226 and RM24 (0.44). Remaining markers were showed less PIC value. Lower PIC value result of closely related landraces and higher PIC values result of diverse landraces. The dendrogram based on UPGMA grouped the 31landraces into 10 clusters that were demarcated at a similarity coefficient of 0.68. Cluster III was the largest including 13 land races followed by cluster VI and II each of which had four and three land races respectively. The remaining clusters had one and two landraces each.

CgSSR marker-based genome-wide association study identified genomic regions for panicle characters and yield in rice (Oryza sativa L.).

To improve production efficiency, positive alleles corresponding to yield-related attributes must be accumulated in a single elite background. We designed and used cgSSR markers, which are superior to random SSR markers in genome-wide association study, to identify genomic regions that contribute to panicle characters and grain yield in this study. As evidenced by the high polymorphic information content value and gene diversity coefficient, the new cgSSR markers were determined to be highly informative. These cgSSR markers were employed to generate genotype data for an association panel evaluated for four panicle characters and grain yield over three seasons. For five traits, 17 significant marker-trait associations on six chromosomes were discovered. The percentage of phenotypic variance that could be explained ranged from 4% to 13%. Unrelated gene-derived markers had a strong association with target traits as well. Trait-associated cgSSR markers derived from corresponding or related genes ensure their utility in direct allele selection, while other linked markers aid in allele selection indirectly by altering the phenotype of interest. Through a marker-assisted breeding approach, these marker-trait associations can be leveraged to accumulate favourable alleles for yield enhancement in rice. © 2022 Society of Chemical Industry.

Genetic Diversity of Eight Native Indonesian Chicken Breeds on Microsatellite Markers

Indonesia has diversity in native chickens based on phenotypes. This diversity is utilized for economic purposes such as meat, eggs, fancy, crowing, and fighting. This study aimed to determine the genetic structure of eight native Indonesian chicken breeds with microsatellite markers, the genetic distance, and inbreeding coefficient of each breed of chicken used for crossbreeding programs to obtain a positive heterosis effect for selection programs. The samples used were Arab, Merawang, Pelung, Sentul, Cemani, KUB, Black Kedu and White Kedu. Broiler chickens (Cobb) were used as the outgroup in this study. A total of 192 DNA samples from eight breeds were used in this study. A total of 24 microsatellite markers were used in this study to observe the genetic diversity of 8 native breeds. The POPGENE, Cervus, and FSTAT were used to generate the observed number of alleles, the effective number of alleles, observed heterozygosity value, expected heterozygosity value, the heterozygote deficit within the breed (FIS), gene flow (Nm), Hardy-Weinberg equilibrium, Polymorphism Information Content (PIC), and UPGMA tree. The principal component analysis (PCA) was performed using adegenet package of R software. Bayesian clustering assignments were analyzed using the STRUCTURE program. This study revealed a very close genetic relationship between seven native chickens and broilers. We also found Arab chickens separated from other Indonesian native chickens and no inbreeding in eight native Indonesian chicken breeds. In conclusion, we found two clusters among eight native Indonesian chicken breeds. Twenty microsatellite markers have a high PIC value in this study.

DNA marker based diversity across rice genotypes and advanced breeding lines bred for temperate regions of North-West India.

Characterization and evaluation of plant genetic resources play an important role for their utilization in the crop improvement programmes. This study involves the agro-morphological and cooking quality besides, molecular characterization of 51 genotypes/advance breeding lines of rice from Kashmir Himalayas. Significant variability was observed for all agro-morphological and cooking quality traits among all the studied genotypes. Cluster analysis using UPGMA method divided the genotypes into two major clusters having 15 and 36 genotypes. Thirty eight genotypes screened using 24 SSR markers detected 48 alleles with 2.0 alleles for each locus with average polymorphism information content (PIC) of 0.37. High polymorphism information content (PIC) values was observed for the primers RM263 (0.67), RM159 (0.59) and RM333 (0.50). Furthermore, out of 38 SSR markers screened on 192 temperate rice germpalsm lines, R4M17 accurately differentiated indica and temperate japonica genotypes amplifying 220bp and 169bp, respectively. Accordingly, 15 genotypes were reported as indica and 28 temperate japonica in addition to 149 genotypes as intermediate types. The information on marker-based diversity and performance based on cooking quality and agronomic traits helped to select the most divergent lines for crossing. Also the analysis was useful to classify the temperate germplasm into indica and temperate japonica. The classification could be helpful to devise a strategy for inter-sub species hybridization to breed for improved rice varieties.

​Cross Genera Marker Transferability and Genetic Diversity Analysis in Elite Cultivars of Mungbean [Vigna radiata (L.) Wilczek

Backgrounds: To increase the accessibility of molecular markers for germplasm evaluation, genetic analysis and new cultivar development in mung bean, cross genera transferability of microsatellites (SSR) was studied. Methods: Forty simple sequence repeat markers developed for adzuki bean were used to amplify genomic DNA extracted from 70 diverse elite cultivars of greengram. Result: All SSR markers (100%) generated repeatable and clear products, signifying a high genomic homology between two species of Vigna. Among the 40 amplified markers, only 11 (28%) were highly polymorphic in 70 diverse elite cultivars of greengram. The polymorphism information content (PIC) ranged between 0.64 to 0.88 with an average of 0.81, while number of alleles ranged with 6 to 12 with an average of 9.27 alleles per locus. The multiple locus amplification and high PIC values indicated the effectiveness of the transferable SSRs in mungbean. Cluster analysis based on UPGMA grouped the studied genotypes into eleven clusters. The Jaccard’s similarity coefficient ranged from 0.17 to 0.46 indicating the extent of transitional amount of genetic variability within the tested genotypes.