Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus

Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus.

Analysis of phenotypic diversity of apricot (Prunus armeniaca L.) accessions from Jammu and Kashmir, India

Apricot (Prunus armeniaca L.) is a world-wide highly appreciated fruit, with its attractive colour, soft texture and typical flavour. In the current investigation, 68 apricot accessions collected from Jammu and Kashmir, India were analysed to determine the measure of variation using 12 qualitative and 16 quantitative traits with an aim to identify superior apricot accessions with excellent fruit quality traits. High phenotypic variability was observed among the studied apricot accessions with significant differences among most of the qualitative and quantitative traits. Fruit-related characteristics including fruit weight, fruit length, fruit ratio, fruit firmness, fruit shape, fruit suture, stone weight, kernel weight and stone shape were the most diverse with a high coefficient of variation (>30%). One way analysis of variance showed significant differences (P < 0.0001) among all the quantitative traits. Significant positive and negative correlations were observed between all the agronomically important fruit quality traits. The principal component analysis (PCA) revealed that 75.34% of the variability was defined by the first eight components. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram, based on all traits measured grouped the accessions into two main clusters with several sub-clusters. Both UPGMA dendrogram and PCA scatter plot formed a cluster of 14 accessions, having the highest values regarding most important fruit quality traits such as fruit weight, fruit length and width, fruit ratio, stone weight and kernel weight can be treated as potentially superior accessions. These accessions can be used directly for cultivation and in future apricot breeding programmes. The present findings are promising for genetic resource management, cultivar improvement and commercial applications of apricot in Jammu and Kashmir, India.

Genetic diversity and relationship between wild and cultivated cowpea [Vigna unguiculata (L.) Walp.] as assessed by allozyme markers

In Cameroon, cowpea plays an important role in traditional agroecosystems. Genetic variation in wild and cultivated cowpea in Cameroon has not yet been documented. Allozyme markers because of their codominance and polymorphism are useful tools for studying genetic variation and disparity in plant species. The present study was undertaken to elucidate the relationship between wild and cultivated cowpea from Cameroon. Ten enzyme systems encoding nineteen isozyme loci were used on 62 cowpea germplasm (45 wild and 17 cultivated). A total of thirty-two alleles were found. One allele was only found in cultivated samples (Enp98 ). Eight alleles were specific only to wild plant (Amp2 98 , Amp3a 103 , Amp4 96 , Fdh104 , Idh2 95 , Pgi3 92 , Pgm2 95 and Sdh95 ). Twenty-three alleles were common to both wild and cultivated accessions. Amp2 10 2 (z = −4.633, p < 0.001) and Fle3 96 (z = −2.858, p < 0.010) were significantly more represented in cultivated compared to wild cowpea forms. The mean number of alleles per locus in wild (1.632 alleles/locus) cowpea were significantly higher (t = 2.805, p < 0.010) compared to cultivated (1.263 alleles/locus) cowpea. Also, the proportion of polymorphic loci (P = 52.63%) and average Nei’s genetic diversity (He = 0.126) were important in wild, compared to the cultivated plants: P = 26.31% and He = 0.063, respectively. The low level of diversity found in domesticated accessions compared to wild can be attributed to a major genetic bottleneck that probably happened during the domestication process. Cluster analysis revealed by UPGMA dendrogram separated the 62 accessions into three clusters. Although an admixture of both wild and cultivated accessions within the same cluster were found, the dendogram, however, highlighted a visible separation between wild and cultivated cowpea. Wild cowpea with many more private alleles indicates an untouched resource available for future breeding.

Target Region Amplification Polymorphism (TRAP) for Assessing Genetic Diversity and Relationships Among Cultivated Populations of Dendrobium officinale

Dendrobium officinale (Orchidacesae) is one of the rare and endangered species of herbs in China. Therefore, it will be beneficial to investigate the genetic diversity and relationships of cultivated populations of D. officinale for quality improvement. In this study, eight target region amplification polymorphism (TRAP) primer combinations were selected from fifty-four combinations, which were designed based on the related genes of the polysaccharides and alkaloids. A total of 148 fragments were scored in nine cultivated populations of D. officinale, including 130 (87.84%) polymorphic fragments. The analysis of genetic diversity revealed high level of genetic diversity in cultivated populations of D. officinale (H = 0.4125, I = 0.5985). Based on analysis of genetic structure, there was a moderate variation (Gst = 0.4706) and lower gene flow (Nm = 0.5625) among the cultivated populations due to some isolated measures, and domestication of excellent cultivars. Moreover, UPGMA dendrogram and Principal Coordinate Analysis (PCoA) indicated that nine cultivated populations were divided into four major groups. The results suggested that genetic relationships were associated with geographical germplasm sources instead of cultivation locations. Therefore, TRAP markers can be effectively employed to analyze genetic diversity and relationships among cultivated populations of D. officinale.

DIVERGÊNCIA GENÉTICA ENTRE GENÓTIPOS DE Mauritia flexuosa L. f. POR MEIO DE MORFOMETRIA DE FRUTOS E SEMENTES

O objetivo do estudo foi caracterizar a variabilidade genética entre vinte genótipos de butiris (M. flexuosa L.f.) em vegetação natural nos municípios de Alta Floresta e Carlinda, MT, com base nas características morfológicas dos frutos e sementes, com o método de Otimização de Tocher, UPGMA e Análise de Componentes Principais. Foram amostrados 20 genótipos e avaliadas 8 caracteres morfológicos dos frutos e sementes. Os resultados foram obtidos através de medidas de Dissimilaridade, com o uso do programa GENES. O método de Tocher formou dois grupos, assim como o agrupamento UPGMA com corte a 80%. Com os Componentes Principais houve a formação de três grupos. As três metodologias utilizadas revelaram que existe divergência genética entre os vinte genótipos de buritis avaliados. A divergência evidenciada neste trabalho permite inferir que para melhor representar a diversidade encontrada em M. flexuosa deve-se amostrar indivíduos pertencentes aos três grupos formados pela dispersão gráfica dos componentes principais, já que o dendrograma UPGMA também evidencia essa classificação, assim, pode-se indicar essas árvores para futuras pesquisas de melhoramento e conservação da espécie. Palavras-chave: buriti; marcadores morfológicos; variabilidade genética. GENETIC DIVERGENCE AMONG Mauritia flexuosa L. f. GENOTYPES BASED ON SEED AND FRUIT MORPHOMETRY ABSTRACT: The objective of the study was to characterize the genetic variability among twenty genotypes of M. flexuosa L. f. in natural vegetation in the municipalities of Alta Floresta and Carlinda, Mato Grosso state, Brazil, based on the morphological characteristics of the fruits and seeds, with the Tocher Optimization method, UPGMA and Principal Component Analysis. Twenty genotypes were sampled and eight morphological characteristics of fruits and seeds were evaluated. The results were based on the Dissimilarities Measures methodology, using the GENES program. The Tocher method formed two groups, as well as the UPGMA cluster with 80% cut. The Principal Components formed three groups. All methods used showed agreement on the formation of groups. The divergence presented in this research allows us to infer that in order to better represent the diversity found in M. flexuosa, individuals belonging to the three groups formed by the graphic dispersion of the principal components must be sampled, since the UPGMA dendrogram also shows this classification, so we indicate these trees for future breeding and conservation researches. Keywords: buriti; morphological characteristics; genetic variability.

Molecular and Phenotypic Characterization for Cold Tolerance in Rice (Oryza sativa L.)

Cold stress affects growth and development of rice plants from germination to reproductive stages. Thirty breeding lines/varieties including tolerant and susceptible check varieties were evaluated for cold tolerance at seedling and reproductive stage using artificially induced low temperature situations to understand the genetic relationship among them and to identify promising donors for cold tolerance. Three breeding lines, BR8253-9-3-4-3, IR77497-31-2-3-1and IR2266-42-6-2 demonstrated higher cold tolerance for the seedling stage (LD score <3.0). Molecular analysis revealed 68% genetic similarity among the genotypes. On average 64% of the breeding lines shared common alleles at any given locus ranging from 27% (RM22870) to 97% (RM186). UPGMA dendrogram showed that majority of the breeding lines showing 4-5 degrees of LD were grouped together. Two breeding lines, BR8258-7-1-5-2B2 and BR8258-7-1-5-2B3 having 86% common alleles showed low leaf discoloration (LD: 4) at seedling stage coupled with relatively low reduction in spikelet fertility (45.8% and 48.1%) and grain yield (43.3% and 39.1%). The gene diversity and PIC value revealed that seven SSR loci (RM1282, RM600, RM5349, RM6972, RM5847, RM5911, and RM511) might be the best markers to differentiate between tolerant and susceptible genotypes at reproductive stage. The breeding lines with tolerance to cold stress at the seedling and the reproductive stages identified from this study, and the SSR markers mentioned above could be useful for developing cold tolerance rice. Bangladesh Rice j. 2019, 23(2): 1-15

Evaluation of Genetic Diversity of Spring Onions (Allium fistulosum) Based on DNA Markers

The Alliaecae family is a widely cultivated vegetable family in Nigeria, with nutritional, culinary and medicinal usefulness. The objective of this study was to assess the genetic diversity using SSR and ISSR markers among ten (10) cultivars of spring onions. This study was carried out using one (1) SSR marker and three (3) ISSR markers. In this study, the genetic diversity among the cultivars were revealed. The four markers produced a total of 26 polymorphic alleles with PIC values of 0.7481, 0.6402, 0.675 and 0.7569 for ISSR 879, ISSR 866, ISSR 881 and SSR 62. The UPGMA dendrogram revealed that the ten spring onion cultivars could be divided into two main groups. The subgroup SPO06 and SPO04 showed no genetic distance among them revealing that there is a very close relationship and in total agreement with the factorial analysis. This study has revealed the efficiency of SSR and ISSR markers to estimate the extent of genetic variation of spring onion cultivars and will be a contribution for the conservation and management of Allium species.

Study of genetic diversity in Tunisian local cattle populations using ISSR markers

The inter-simple DNA sequence repeat (ISSR) method was used to study genetic diversity in three local cattle from the north, northeast and north west of Tunisia. Twenty samples were analysed using three ISSR primers. In total, 22 bands were amplified of which 15 are polymorphic (68.18%). The total genetic diversity (Ht), genetic diversity within populations (Hs), coefficient of gene differentiation (Gst) and gene flow (Nm) were 0.2706, 0.01314, 0.8841 and 0.0656. To better visualize the structure of the population, a UPGMA dendrogram constructed from the genetic distances of NEI shows that the populations of North (Bizerte) and Northeast (Nabeul) are genetically closest while that of Northwest (Jendouba and Siliana) is the furthest from the two others.

GENETIC DIVERSITY OF Brassica rapa GERMPLASM OF KHYBER PAKHTUNKHWA PAKISTAN REVEALED BY MOLECULAR MARKERS

A total of 96 indigenous Brassica rapa accessions were collected from different locations of Khyber Pakhtunkhwa, Pakistan. Simple Sequence Repeats (SSR) markers were used to identify the most diverse genotypes among the collected lots. Twenty six (26) different SSR primers were used for (genetic) variability among collected genotypes. These primers were selected from literature based on their previous results. These primers produced 135 scorable bands of which 75 were polymorphic, with an average of 55.5% polymorphic loci, and reflected the broader genetic background of the collected genotypes. An average 2.88 polymorphic bands with an average PIC value of 0.49 was recorded. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) divided all genotypes into three main groups. Group one contained three clusters, while group two and three had four and two clusters each. Based on the UPGMA dendrogram, genotypes collected from Kohat, Bannu, Swat and Haripur showed considerable amount of variation. From the present study, it is concluded that SSR markers can be proved as the best tool for the genetic variability of other local and exotic B. rapa genotypes.

Effect of LCORL gene polymorphism on body size traits in horse populations

The aim of this study was to determine polymorphism of LCORL gene in horse breeds and its association with body size. PCR-RFLP technique was performed using AluI for genotyping of 306 horses. Results showed that C is the rare allele in Iranian Breeds, because these horses have been used since ancient times as a courier and for war and archery, hence selection has done to benefit of spiky horses with medium body that need less food and are tireless. While, for foreign breeds; frequency of C allele was high that can be concluded these breeds used in fields, forests, and mines. A UPGMA dendrogram based on the Nei's standard genetic distance among studied breeds showed separate clusters for Iranian native and exotic breeds. Statistical association analysis of three observed genotypes with body size showed that there is an association between this polymorphism and body size criteria (p < 0.01). Overall, it can be concluded that studied mutation in LCORL gene can be used as candidate marker for improving body weight in horse.