DNA Marker Based Diversity Across Rice Genotypes and Advanced Breeding Lines Bred for Temperate India

Background: Characterization and evaluation of plant genetic resources play an important role for their utilization in the crop improvement programmes. Methods and results: This study entails the agro-morphological, cooking quality and 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 per locus and an 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 220 bp and 169bp, respectively. Accordingly, 15 genotypes were reported as indica and 28 temperate japonica in addition to 149 genotypes as intermediate types. Conclusion: The information on marker-based diversity and performance based on cooking quality and agronomic traits helped to select the most divergent lines for crossing and also the analysis was useful to generate information on indica - japonica classification of our germplasm.

Genetic diversity of Clarias anguillaris from the Bakoye River in Mali

Clarias anguillaris is a wild species found in River basins in Mali. It is the species most commonly used in fish farming in community stockings. However, it excites little study on the genetic diversity of this species in the natural environment in Mali. The present study focused on the genetic diversity of Clarias anguillaris from the Bakoye River, a tributary of the Senegal River in Mali. A total of (8) microsatellite markers were applied to 47 samples taken at random from the River. The markers were Cga02, Cga03, Cga06, Cga10, Cba11, Cba19, Cba20 and Cma12. The number of alleles, the number of genotype, genetic diversity, Polymorphism Information content (PIC), observed and expected heterozygosity were determined. The results showed that the number of alleles ranged from 1 to 7, with an average of 4.25 per locus. The mean rate of observed heterozygosity was 0.34 lower than that of expected heterozygosity which was 0.48 indicating nonconformity of the Hardy-Weinberg equilibrium. The allele frequency ranged from 0.35 at the Cba19 locus to 1 at the Cba11 locus, with a mean of 0.62. Genetic diversity ranged from 0 for Cba11 to 0.75 for Cba19. The markers Cga02, Cga03, Cga06, Cba19, Cba20 and Cma12 were polymorphic with an average peak of 0.42. The phylogenetic tree presented two groups of genotypes showing diversity within the species. Group I comprised 60.42% of individuals and group II presented 39.58% with 3 subgroups (A, B and C). The genetic distance (0.05) indicates little differentiation between individuals.

Detection of A1 and A2 Alleles at Beta-casein Locus in Bargur and Umblachery (Indian Zebu) Cattle Breeds by Allele-specific PCR

Background: Many genetic variants of beta-casein in different breeds of cattle have been reported. The A1 and A2 are the most common variants. The breeds of Zebu cattle have high frequency of A2 allele or monomorphic for A2 allele. The current study aimed to screen Indian Zebu cattle breeds, Bargur and Umblachery, for A1 and A2 alleles at beta-casein locus.Methods: A total of 48 Bargur and 42 Umblachery cattle were genotyped for β-casein (CSN2) gene using allele-specific PCR. The gene and genotype frequencies were estimated. The theoretical heterozygosity (Heexp), experimental heterozygosity (Heobs), polymorphism information content (PIC), expected homozygosity (E), effective number of alleles (ENA) and level of possible variability realization (V%) were calculated.Result: The investigation revealed the presence of both A1 and A2 alleles at beta-casein locus in both Bargur and Umblachery cattle breeds. The A1A1 genotype was not observed in both the breeds. The frequencies of A1A2 and A2A2 genotypes were 0.125 and 0.875 respectively in Bargur and 0.050 and 0.950 respectively in Umblachery breed. The study indicated the predominance of A2 variant in both the breeds. The frequencies of A1 and A2 alleles were 0.063 and 0.937 respectively in Bargur and 0.02 and 0.98 respectively in Umblachery breed. The values of experimental heterozygosity (Heobs), theoretical heterozygosity (Heexp), polymorphism information content (PIC), expected homozygosity (E), effective number of alleles (ENA), level of possible variability realization (V%) were 0.125, 0.1163, 0.1095,0.8837, 1.131 and 11.88 respectively in Bargur breed. These values were 0.048, 0.0468, 0.0458, 0.9532, 1.049 and 4.79 respectively in Umblachery population. The observed heterozygosity and PIC values revealed the existence of very low genetic variability in the tested populations. The present work will be a contribution to the study on beta-casein locus in Indian zebu cattle.

Development and Characterization of 68 Microsatellite Markers of Black Amur Bream Megalobrama terminalis by Next-Generation Sequencing

This study developed and characterized 68 novel polymorphic microsatellite markers from black Amur bream Megalobrama terminalis by next-generation sequencing. Variability was tested on 36 individuals collected from Qiantang River, Zhejiang Province, China. The number of alleles per locus ranged from 2 to 13. Observed heterozygosity ranged from 0.028 to 0.944, whereas the expected heterozygosity ranged from 0.028 to 0.887. Polymorphism Information Content ranged from 0.027 to 0.862. Moreover, 53 microsatellites were in agreement with Hardy–Weinberg equilibrium. Twenty-eight pairwise tests in 33 microsatellite loci indicated linkage disequilibrium. These microsatellites are a valuable tool for further genetics studies of this species.

Keragaman Genetik 27 Aksesi Kedelai (Glycine Max L. Merr.) Introduksi Subtropis berdasarkan Marka SSR

Karakterisasi aksesi kedelai (Glycine max L. Merr.) dalam koleksi perlu dilakukan berdasarkan marka molekuler untuk mendukung karakter morfologi. Penelitian ini bertujuan untuk menganalisis keragaman genetik aksesi kedelai yang diintroduksi dari daerah subtropis menggunakan marka simple sequence repeats (SSR) yang didukung melalui informasi karakter morfologi. Hasil penelitian menunjukkan bahwa sebanyak 15 SSR berhasil dideteksi polimorfismenya pada 27 aksesi kedelai dari daerah subtropis dengan total 158 alel berukuran antara 100-368 bp dengan kisaran jumlah 4-18 alel per lokus. Rata-rata polymorphism information content (PIC) ditemukan sebesar 0,92 dengan nilai tertinggi 0,96 (SATT463, SATT249, SATT063) dan nilai terendah 0,87 (SATT038). Semua marka SSR memiliki nilai PIC >0,8 yang mengindikasikan sebagai marka sangat informatif, artinya mampu mendiferensiasi antar aksesi dan dapat diaplikasikan dalam mendeteksi keragaman genetik plasma nutfah kedelai lainnya. Keragaman genetik aksesi kedelai terebut sangat tinggi seperti yang direfleksikan oleh rata-rata indeks diversitas gen sebesar 0,93. Analisis klaster dengan marka SSR berhasil membagi 27 aksesi kedelai menjadi dua kelompok utama yang sebagian besar dalam kelompok I (26 aksesi) dan kelompok II khusus aksesi D76-8070. Karakterisasi molekuler dengan SSR tersebut mendukung keragaman yang tinggi karakter morfologi yang memisahkan total aksesi menjadi empat kuadran. Informasi keragaman genetik berdasarkan marka S yang didukung karakter morfologi tersebut dapat menjadi dasar awal seleksi tetua persilangan aksesi dari daerah subtropis untuk pengembangan varietas baru melalui pemuliaan kedelai di iklim tropis Indonesia.

Study of genetic diversity in oat accessions identified using of SSR markers

Oat is an important cereal crop for the food and feed industries. Genetic resources of oat are the basic materials for sustainable breeding programs. Microsatellites (SSR) are a useful tool for understanding the genetic background of oat germplasm resources. We used 83 SSR primer pairs to assess the genetic diversity of 286 oat accessions from five countries. The results indicated the presence of considerable variation among accessions. The number of alleles per SSR locus ranged from 2 to 8, with an average of 3.49; allelic frequencies ranged from 0.002 to 0.709; Nei’s gene diversity was 0.67, ranging from 0.44 to 0.85; and polymorphism information content (PIC) values ranged from 0.37 to 0.83. Six groups were separated by cluster and structure analyses indicating the relationships between accessions with different origins. Хошуу будааны генетикийн oлон янз байдлыг SSR маркер ашиглан тодорхойлсон судалгаа Хошуу будаа (Avena L.) нь хүнс, тэжээл үйлдвэрлэлийн чухал үр тарианы таримал юм. Хошуу будааны генетикийн олон янз байдал түүний селекцийг чанартай явуулах үндсэн гол чухал материал болдог. SSR маркер ашиглан хошуу будааны үр хөврөлийн (germplasm) олон янз байдал, түүний генетикийн үндэсийг тодорхойлж болдог. Бид судалгаандаа 83 хос SSR праймер ашиглан 5 өөр улсын 286 хошуу будааны дээжийн генетикийн олон янз байдлыг үнэлэн тогтоолоо. Судалгааны үр дүнгээс харвал дээжүүдийн хоорондын генетикийн ялгаа өндөр байв. SSR маркерын байршил дахь аллелийн тоо 2-8, дунджаар 3.49, харин тойргийн аллелийн давтамж 0.002-0.709, Nei-ийн төрөл зүйл 0.67 байсан бол тойрог нь 0.44-0.85, полиморфизмын мэдээллийн агуулга (PIC) 0.37-0.83 хооронд хэлбэлзэж байв. Зургаан бүлгийг кластер болон бүтцийн дүн шинжилгээгээр тусгаарласан бөгөөд өөр өөр гарал үүсэлтэй дээжүүдийн хоорондох хамаарлыг үзүүллээ. Түлхүүр үг: Хошуу будаа, генетикийн олон янз байдал, SSR маркер

A Global Analysis of Y-STR INRA189 Polymorphism in Chinese Domestic Yak Breeds/Populations

The objective of this study was to probe into the polymorphism of Y-STR INRA189 and identify the geographical distribution pattern of its alleles in the Chinese domestic yak gene pool. We examined the variation at INRA189 locus in 682 male yaks representing 15 breeds/populations in China. The results showed that six alleles, including five reported previously (149, 155, 157, 159, and 161 bp) and a new one identified in this study (139 bp), were detected at INRA189 locus based on genotyping analysis. The frequencies of six alleles varied among the 15 yak breeds/populations with a clear phylogeographical pattern, which revealed the paternal genetic difference among Chinese yak breeds/populations. The average polymorphism information content (PIC) among the 15 yak breeds/populations was 0.32, indicating INRA189 to be an intermediate polymorphic Y-STR marker (0.25 < PIC < 0.5) in yak. Sequence alignment revealed that the variations among six alleles at INRA189 were defined by a TG dinucleotide repeat motif, which repeated for 12, 17, 20, 21, 22, and 23 times, corresponding to the alleles of 139, 149, 155, 157, 159, and 161 bp, respectively. Therefore, we believe that the polymorphic yak Y-STR INRA189 can be used to characterize male-mediated genetic events, including paternal genetic origin, diversity, and evolution.

Genetic analysis of DXS101and DXS6807 short tandem repeat (X-STR) in samples of Iraqi Arab male population

Back ground: X-chromosomal short tandem repeats (X-STRs) have assured to be informative and particular role in complex relationship testing. DXS6807 known as tetra nucleotides polymorphism representing eight alleles of 251-275 bp in length. DXS6807 is located in, at XP 22.2, at a genetic distance of more than 87 and 151 Cm of X-chromosome. DXS101 is located104.9–121 cM from the Xp-telomere (Xp-tel) corresponding to cytogenetic position in Xq21.33–Xq22.3. Objective: The aim of this present study investigates the allele frequency of two markers DXS101, DXS6807 and forensic efficiency parameters for sample of Arabic Iraqi males. Material and methods: The population of this study includes 200 males apparently healthy unrelated participants from different region of Baghdad city, their ages ranged between (20-50) years. The Genomic DNA extracted and purified successfully from blood samples. Results: The forensic efficiency parameters result for these markers were following: polymorphism information content (PIC) of 0.834708, power of discrimination (PD) in male 0.851750, Power of exclusion (PE) 0.698316, MEC Krüger0.511679, MEC Kishida 0.694890. The forensic efficiency parameters analyzing from Arabic population were Power of discrimination (PD) = 0.73405, Polymorphism information content (PIC) =0.69489, Power of exclusion (PE) =0.482879.MEC Krüger =0.511679, MEC Kishida = 0.694890. Conclusions: The information provided establish this X-linked microsatellite marker as a valuable strategy for forensic application. DXS101is and DXS6807 recently consider more stable and suitable forensic markers for forensic application.

An Evaluation of the Genetic Structure of Geese Maintained in Poland on the Basis of Microsatellite Markers

The aim of this study was to evaluate the genetic variability of the White Kołuda® goose and 12 conservative flocks: Kielecka, Podkarpacka, Garbonosa, Pomerian, Rypinska, Landes, Lubelska, Suwalska, Kartuska, Romanska, Slowacka, and Kubanska, maintained in Poland using microsatellite data. The genetic diversity of geese kept in Poland remains poorly analyzed at the molecular level. In total 392 samples were examined with the usage of 15 microsatellite markers. 119 alleles were identified and the number of alleles per locus ranged from 1 to 13. The highest number of alleles was observed in TTUCG5 (16) and the lowest in CAUD-G007 (2), while CKW47 was monomorphic. The lowest value of expected heterozygosity (He) was observed in Landes, while the highest in Romanska. Similarly, the observed heterozygosity (Ho) was the lowest in Landes but the highest in Kartuska. The polymorphism information content (PIC) indicates loci TTUCG5 as the most valuable microsatellite marker among those examined. The Structure software was used for the first time to identify goose populations, revealing high admixture between breeds and their close genetic propinquity. Moreover, the presented panel of microsatellite markers remained polymorphic and is useful for population studies of geese and assessment of genetic diversity.