Development of SSR Markers and Genetic Diversity Evaluation of Mycocentrospora Acerina Causing Round Spot of Panax Notoginseng in Yunan Province, China

Sanqi round spot, which is caused by Mycocentrospora acerina, is a destructive disease limits the production of Panax notoginseng in Yunnan province of China. However, the disease has not been studied comprehensively. In the current study, we identify M. acerina polymorphic microsatellite markers using CERVUS 3.0 and compare the genetic diversity of its isolates from P. notoginseng round spot using Simple Sequence Repeat (SSR) markers and polyacrylamide gel electrophoresis. Thirty-two SSR markers with good polymorphism were developed using MISA and CERVUS 3.0. The genetic diversity of 187 M. acerina isolates were evaluated using 14 representative SSR primers, and the polymorphic information content values of 14 sites ranged from 0.813 to 0.946, with a total of 264 alleles detected at 14 microsatellite loci. The average expected heterozygosity was 0.8967. The genetic diversity of M. acerina in Yunnan province does not reflect geographic specificity.

Schinus Terebinthifolia Raddi: A Comparative Framework On Population Genetic Structure In A Restored Area After 12 Years*

The success of restoration projects depends upon the genetic diversity of the implanted species. It is a limiting factor, often because the seed sources are immersed in highly fragmented landscapes. This work was carried out to compare the genetic diversities of the juveniles and the adult trees of Schinus terebinthifolia Raddi in a mixed reforestation area, both in the restoration process and in the remaining natural area in the Atlantic Forest. Through five SSR primers, it was observed that the implanted population showed a greater genetic diversity index (He) (0.553 adults and 0.505 juveniles) when compared to the wild population (0.487 adults and 0.483 juveniles). It indicated that the forested area was established with individuals of high genetic diversity. There was a reduction of genetic diversity, with the loss of exclusive alleles and maintenance of inbreeding and coancestry in the juveniles of the reforested population. It can be inferred that there was a low gene flow among the fragments. The effective population size in both populations (adults and juveniles) was lower than that recommended for conserving populations in the short and long terms. These results have shown that continuous monitoring of this particular area is of absolute necessity and for applying techniques that can promote the connectivity of the fragments. It would allow for a more significant reduction of genetic drift and the persistence of the planted populations.

ĐA DANG DI TRUYỀN CỦA 120 GIỐNG/DÒNG ĐẬU NÀNH (Glycine max (L.) Merr.) BẰNG CHỈ THỊ PHÂN TỬ SSR

Nghiên cứu đa dạng di truyền nhằm mục đích tìm ra mối quan hệ giữa các kiểu gen trong tập đoàn giống/dòng cây trồng, từ đó có thể đưa ra chiến lược chọn tạo giống, cải thiện nguồn gen. Nghiên cứu này đã sử dụng 09 chỉ thị phân tử SSR để đánh giá mức độ đa dạng di truyền của 120 giống/dòng đậu nành (Glycine max (L.) Merr.) đang được bảo tồn tại ngân hàng giống trường Đại học Cần Thơ. Kết quả điện di sản phẩm PCR bằng 09 chỉ thị phân tử SSR thu được 52 phân đoạn và tất cả 52 phân đoạn đều có tỷ lệ đa hình trung bình cao (100%). Chỉ số PIC dao động từ 0,05 (satt596) đến 0,46 (satt009), với giá trị trung bình là 0,21. Cây phả hệ được xây dựng dựa trên 09 chỉ thị SSR bằng phân tích nhóm UPGMA phân các mẫu thành 11 nhóm chính với hệ số di truyền trung bình là 0,7 và hệ số tương đồng dao động từ 0,47 - 0,87. Kết quả này cho thấy bộ sưu tập 120 giống/dòng đậu nành rất đa dạng về bản chất di truyền và có thể dùng làm vật liệu ban đầu cho công tác chọn tạo giống đậu nành trong tương lai. ABSTRACT Genetic diversity research aims to study the relationship between genotypes in the varieties/lines, as the results, a breeding strategy will be set up for genetic improvement. In this study, 09 SSR molecular markers were used to evaluate the genetic diversity of 120 soybean varieties/lines being conserved at the gene bank of Can Tho University. A total of 52 fragments were produced by 09 SSR primers with 100% polymorphism rate. The PIC index value was ranged from 0.05 (satt596) to 0.46 (satt009), the average PIC index was 0.21. Using UPGMA analysis showed that the phylogenetic tree was divided 120 soybean varieties/lines into 11 main groups with the average genetic coefficient of 0.7 and the similarity coefficient ranging from 0.47-0.87. Thus, this result showed that the collection of 120 soybean varieties/lines is very diverse in genetic background and can be used as a starting material for future soybean breeding.

Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers

Vicia amoena is a high-nutritional quality forage similar to alfalfa. However, studies on the genetic background of V. amoena are scarce. In the present study, the genetic variation of 24 V. amoena populations was assessed with newly developed simple sequence repeat (SSR) markers. A total of 8799 SSRs were identified in the V. amoena genomic-enriched sequences, and the most abundant repeat number was four. A total of 569 sampled individuals were assayed to evaluate the genetic diversity of the V. amoena populations based on 21 polymorphic SSR primers. The polymorphism information content (PIC) ranged from 0.896 to 0.968, with an average of 0.931, which indicated that the markers were highly informative. Based on analysis of molecular variance, 88% of the variance occurred within populations, and the remaining 12% of the variance occurred among populations. The high degree of gene flow (Nm= 4.958) also showed slight differentiation among the V. amoena populations. The V. amoena populations were mainly clustered by steppe and mountain habitats based on principal coordinate analysis (PCoA) and STRUCTURE analysis. This indicated that the elevation and special habitat of geographical origins may be important factors affecting the clustered pattern of V. amoena populations. Neighbour-joining (NJ) analysis did not separate the populations well by geographical origin, which indicated that the genetic structure of V. amoena was complex and needs further study. Overall, our results showed that the newly developed SSR markers could benefit the V. amoena research community by providing genetic background information to help establish a foundation for breeding improvement and germplasm resource conservation.

Genetic and Morphological Variability among the Isolates of Fusarium oxysporum f. sp. lentis causing Wilt of Lentil

Background: Lentil wilt is one of the most important diseases of lentil directly contributing to the yield losses of the crop. It is caused by Fusarium oxysporum f. sp. lentis which shows the great genetic and morphological diversity. Methods: Present investigation was conducted during 2017-2019 with 22 isolates of the pathogen, collected from lentil grown areas of Uttarakhand and Uttar Pradesh to explore genetic and morphological variability employing eight ISSR and five SSR primers. Result: The isolates showed huge morphological variability based on the color, pigmentation and shape of conidia. Study on molecular variability revealed the versatility in the genome of different isolates of pathogen. The diversity among the isolates of pathogens collected from Uttarakhand and Uttar Pradesh was also evident. Generated work on genetic and morphological variability and the population diversity among the different isolates of the pathogen impact on developing ideal disease management strategies.

Estimation of Genetic Diversity among Canola Accessions using Simple Sequence Repeat Markers

Genetic studies through molecular markers proved important to find out the genetic diversity of canola. In this study, 50 lines of canola were used to find the polymorphism using 15 SSR primers and investigated the genetic diversity, PIC values, frequency-based genetic distance, and allelic frequencies. Mean gene diversity, frequency-based genetic distance, and PIC values were 0.8777, 0.233 and 0.8666, respectively for the canola lines. A good range of genetic diversity was found among studied canola lines with value 85.91% polymorphism. Maximum and minimum genetic distances among 50 lines were 1 and 0.26, respectively. Accessions ACC-26068, ACC-24241, ACC-24244, ACC-24233, ACC-24423 and ACC-24224 have maximum genetic distance. Accessions ACC-24879 and ACC-24169 had minimum genetic distance i.e., 0.26. Dendrogram based on genetic distances showed four main clusters that were further dividing into several sub-clusters. The primers utilized in the present study, were valuable to identify different accessions of canola to find the variability present. This variability will be helpful to initiate the breeding program with their molecular genetic basis.

Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.)

Ginger (Zingiber officinale Rosc.) is an economically important and valuable spice crop around the world. It is used as food, spice, condiment, and medicine. A considerable extent of genetic diversity in ginger occurs in the Western Ghats and North-Eastern India. However, genetic diversity studies at the molecular level in ginger is limited due to limited availability of genetic and genomic information. In the present study, for the first time, we have identified and validated expressed sequence tag (EST)-simple sequence repeat (SSR) markers from ginger. We obtained 16,790 EST-SSR loci from 78987 unigenes, and 4597 SSR loci in the predicted 76929 coding sequences from RNA-Seq assembled contigs of ginger through Illumina paired-end sequencing. Gene ontology results indicate that the unigenes with SSR loci participate in various biological processes such as metabolism, growth, and development in ginger. One hundred and twenty-five primer pairs were designed from unigenes and coding sequences. These primers were tested for PCR optimization, characterization, and amplification and identified 12 novel EST-SSR markers. Twelve flanking polymorphic EST-SSR primers were validated using 48 ginger genotypes representing North-Eastern India and different eco-geographical adaptations by PCR amplification and allele sizing through capillary electrophoresis. Twelve EST-SSR primers generated a total of 111 alleles with an average of 9.25 alleles per locus and allele sizes ranging between 115-189bp. This study implies that the SSR markers designed from transcriptome sequences provides ample EST-SSR resources, which are helpful for genetic diversity analysis of Zingiberaceae species and molecular verification of ginger genotypes.

Genetic Diversity of Cassava (Manihot esculenta Crantz) in Ecuador by Using SSR Markers

Cassava (Manihot esculenta Crantz), domesticated in the Amazonian region of South America, presents an important diversity in Ecuador, where it is a main staple food; however, only few Ecuadorian cassava accessions have been included in international molecular assessments. The purpose of this study was to apply suitable cassava mi-crosatellites to characterize the genetic variability of the Ecuadorian cassava collection composed mainly of local landraces from the Coast, Andes and Amazonia regions. The use of microsatellite markers allowed the determination of the genetic diversity of the collection. Seven selected SSR primers, permitted to identify homozygous and hetero-zygous materials within the cassava collection of 133 accessions. The loci presented an average genetic diversity value of 0.7 and an average PIC value of 0.67, which is con-sidered high. Low number of duplicates (8.8%) were identified in the Ecuadorian col-lection which is not fully duplicated at CIAT. Currently, a wide range of cassava diver-sity is still cultivated in multi-crop agro-ecosystem, mainly in the Coast and Amazo-nian regions. Especially in the Amazonian region, due to important cultural uses of cassava by local ethnic communities, more in depth studies in the region could unveil the genetic diversity present in situ today.

Development of Genome-wide Simple Sequence Repeat Markers from Whole-genome Sequence of Mungbean (Vigna radiata)

Background: Mungbean is an important pulse crop and it is mainly cultivated in Asia for human consumption. Its small genome and diploid nature make it a well-suited model organism among legume crops. Thus, cost-effective, reliable and highly polymorphic molecular markers distributing the whole genome are needed for diversity, mapping and functional genomics studies in this model species. Methods: The whole-genome sequence of mungbean was obtained and used as a source of identification of simple sequence repeats (SSR). The sequence reads were aligned and SSRs detection was performed using the Phobos plugin tandem repeat finder in the Geneious software program. A total of 12 mungbean genotypes were selected to validate the newly developed SSR markers. Result: In the present study, a total of 12, 49,774 and 11, 86, 386 perfect and imperfect SSR repeats were identified from the mungbean genome. The tri-repeats were the most abundant (26.10%), followed by hexa (20.82%), penta (20.45%), tetra (17.65%) and di-repeats (14.95%). We designed 1330 SSR primers based on the genomic sequence of flanking perfect SSRs (Di and tri-repeats). Among them, 50 SSR primers uniformly distributed across the 11 mungbean chromosomes were selected and used to validate 12 mungbean genotypes. The newly developed genomic SSR markers generated in the present study are a valuable genomic resource for the mungbean breeding programs.

Genetic diversity of sugar palm (Arenga pinnata) derived from nine regions in Indonesia based on SSR markers

Rinawati DY, Reflinur, Dinarti D, Sudarsono. 2021. Genetic diversity of sugar palm (Arenga pinnata) derived from nine regions in Indonesia based on SSR markers. Biodiversitas 22: 3749-3755. Sugar palm (Arenga pinnata (Wurmb) Merr.) has an important economic and conservation value. Indonesia has genetic diversity potential of sugar palm, considering the widespread distribution of sugar palm in Indonesia which has variations in geographical type. This study aims to determine the diversity and relationship of sugar palm from nine regions in Indonesia based on SSR markers. The genetic material consists of 141 sugar palm accessions derived from Bangka, Lampung, Lebak, Bogor, Tasikmalaya, Brebes, Gowa, Bombana, and Muna. Nine pairs of SSR primers were used for genotyping. The highest and lowest genetic diversity was found in the Bangka and Muna populations, respectively. The genetic diversity within a population (79%) was higher than the genetic diversity between populations (21%). The genetic distance between Bangka and Lebak is the closest (0.033), while between Lampung and Muna is the farthest (0.283). The accession relationship is divided into three major clusters. Clusters 1 consisted of Bangka, Lampung, Bogor, Tasikmalaya, Brebes, Gowa, Bombana and Muna accessions. Cluster 2 consisted of Bangka, Lampung, Lebak, Bogor, Tasikmalaya, Brebes, and Gowa accessions. Cluster 3 consisted of Bangka, Lebak, Brebes, Tasikmalaya, and Gowa accessions. Accession clustering does not show a typical relationship pattern based on geographic location.