Genome-Wide Assessment of Population Structure and Genetic Diversity of the Global Finger Millet Germplasm Panel Conserved at the ICRISAT Genebank

Finger millet [Eleusine coracana (L.) Gaertn.] is an important climate-resilient nutrient-dense crop grown as a staple food grain in Asia and Africa. Utilizing the full potential of the crop mainly depends on an in-depth exploration of the vast diversity in its germplasm. In this study, the global finger millet germplasm diversity panel of 314 accessions was genotyped, using the DArTseq approach to assess genetic diversity and population structure. We obtained 33,884 high-quality single nucleotide polymorphism (SNP) markers on 306 accessions after filtering. Finger millet germplasm showed considerable genetic diversity, and the mean polymorphic information content, gene diversity, and Shannon Index were 0.110, 0.114, and 0.194, respectively. The average genetic distance of the entire set was 0.301 (range 0.040 – 0.450). The accessions of the race elongata (0.326) showed the highest average genetic distance, and the least was in the race plana (0.275); and higher genetic divergence was observed between elongata and vulgaris (0.320), while the least was between compacta and plana (0.281). An average, landrace accessions had higher gene diversity (0.144) and genetic distance (0.299) than the breeding lines (0.117 and 0.267, respectively). A similar average gene diversity was observed in the accessions of Asia (0.132) and Africa (0.129), but Asia had slightly higher genetic distance (0.286) than African accessions (0.276), and the distance between these two regions was 0.327. This was also confirmed by a model-based STRUCTURE analysis, genetic distance-based clustering, and principal coordinate analysis, which revealed two major populations representing Asia and Africa. Analysis of molecular variance suggests that the significant population differentiation was mainly due to within individuals between regions or between populations while races had a negligible impact on population structure. Finger millet diversity is structured based on a geographical region of origin, while the racial structure made negligible contribution to population structure. The information generated from this study can provide greater insights into the population structure and genetic diversity within and among regions and races, and an understanding of genomic-assisted finger millet improvement.

Using SSR markers for evaluation of genetic variation among sesame (Sesamum indicum L.) accessions

Sesame (Sesamum indicum L.) is an annual plant belonging to the Pedaliaceae family which is the oldest of the oilseed plants. Sesame is known as the king of oilseeds because its seeds contain high oil content (50-60%). The objective of the study was to evaluate the genetic variation of sesame accessions based on ten SSR markers. The results showed that all sesame accessions showed high genetic similarity among individuals in each accession. Polymorphism information content ranged from 0.24 (TNB17) to 0.37 (MT20). HO varied from 0.04 (MT30) to 0.25 (GENE1). The highest HE was 0.37 (MT20) and the lowest HE was 0.28 (TNB17). The results also displayed the high genetic diversity among 7 sesame accessions. The genetic diversity distance varied from 0.0 to 1.0. Dendrogram analysis divided 7 sesame accessions into 5 clear groups at an average genetic distance of 0.25. The results achieved would be useful information for genetic evaluation and sesame breeding development in the future.

GENETIC OF Panulirus versicolor LOBSTER IN CENDRAWASIH BAY PAPUA AND LOMBOK WATERS WEST NUSA TENGGARA

The purpose of this study was to determine the level of diversity and genetic relationship of Panulirus versicolor lobsters in Cenderawasih Bay and Lombok waters based on the cytochrome oxidase I (COI) gene. The results showed the level of genetic diversity of the two populations was very high and generally did not differ greatly between populations. We identified 6 haplotypes for P. versicolor lobster populations from Cenderawasih Bay and 7 haplotypes for P. versicolor lobster populations from Lombok waters. Network analysis shows that several P. versicolor lobster individuals from the Cendeawasih Bay and Lombok waters had similar haplotypes. The population of Cenderawasih Bay with Lombok waters was closely related to the average genetic distance value P-distance 0.005 (s.d 0.001) and the results of phylogenetic tree reconstruction showed that the two populations of P. versicolor lobsters form a monophyletic clade (close relatives).

Genetic variants of parvovirus B19 circulating in Belarus during the epidemic cycle of infection (2005–2016)

Human parvovirus infection is characterized by a variety of clinical manifestations. Based on the genetic analysis, genotypes 1a, 1b, 2, 3a, 3b of parvovirus B19 are distinguished, which have different geographical distribution. In the period 2005–2016, in Belarus 210 strains of parvovirus B19 isolated from the patients with various forms of parvovirus infection, mainly erythema infectiosum, were genotyped. All strains, except one, belonged to genotype 1a. One strain belonged to genotype 3b and was isolated from a child with aplastic crisis who arrived in Belarus from Kazakhstan for medical care. On the phylogenetic tree, the strains of genotype 1a formed two groups related to the subtypes 1a1 and 1a2. During the 12-year observation, both subtypes circulated in Belarus, but with varying intensity. In the highest incidence years, as well as one or two years before and after this (2005–2008 and 2013–2016), strains of subtype 1a2 predominated in circulation. During the period of low incidence (2009–2012), the dominant position belonged to subtype 1a1. The average genetic distance inside each subtype was 0.51 % for 1a1 and 0.56 % for 1a2. Between subtypes it was also small – 1.32 %. It can be assumed that subtype 1a2 is more new for Belarus and therefore might be connected with the increase of morbidity.

Phylogenetic relationships of Scelimeninae genera (Orthoptera: Tetrigoidea) based on COI, 16S rRNA and 18S rRNA gene sequences

Scelimeninae is an important subfamily of Tetrigoidea; however, the phylogenetic relationships within Scelimeninae are poorly understood, and its generic classification has remained unstable. In this study, the COI, 16S rRNA and 18S rRNA genes from 24 species in 9 genera within Scelimeninae were amplified and sequenced, the base composition and inter-species genetic distance of the combined sequence of COI, 16S rRNA and 18S rRNA genes were analyzed, and the molecular phylogenetic relationships were reconstructed using Maximum Likelihood (ML) and Bayesian inference (BI) methods. The results of sequence analysis showed that the total length of the combined COI, 16S rRNA and 18S rRNA gene sequence was 3507 bp, including 2345 conservative sites, 1144 variable sites and 901 parsimony-informative sites. The average A+T content was 63.5% and 78.1% in the COI, 16S rRNA sequences, respectively, indicating A+T bias. The average genetic distance between all species was 0.134, and the average genetic distance in the inner group (Scelimeninae) was 0.126. A phylogenetic tree based on the combined sequences of the COI, 16S rRNA and 18S rRNA genes showed that the phylogenetic relationships among 9 Scelimeninae genera were as follows: Criotettix + (((Zhengitettix + Hebarditettix) + (Falconius + (Scelimena + Paragavialidium))) + ((Eucriotettix + Thoradonta) + Loxilobus)). The molecular phylogenetic results generally support the morphological taxonomy; at the genus level, Criotettix, Scelimena, Paragavialidium, Thoradonta and Eucriotettix are monophyletic groups, Scelimena and Paragavialidium form sister groups, and Thoradonta and Eucriotettix also form sister groups, but the relationship between Hebarditettix and Zhengitettix needs further study. At the species level, synonyms may exist between Thoradonta spiculoba and Thoradonta transpicula and Thoradonta nodulosa and Thoradonta obtusilobata, but more studies are required to confirm this inference.

A Predominant Variable-Number Tandem-Repeat Cluster of Mycobacterium tuberculosis Isolates among Asylum Seekers in the Netherlands and Denmark, Deciphered by Whole-Genome Sequencing

ABSTRACT In many countries, Mycobacterium tuberculosis isolates are routinely subjected to variable-number tandem-repeat (VNTR) typing to investigate M. tuberculosis transmission. Unexpectedly, cross-border clusters were identified among African refugees in the Netherlands and Denmark, although transmission in those countries was unlikely. Whole-genome sequencing (WGS) was applied to analyze transmission in depth and to assess the precision of VNTR typing. WGS was applied to 40 M. tuberculosis isolates from refugees in the Netherlands and Denmark (most of whom were from the Horn of Africa) that shared the exact same VNTR profile. Cluster investigations were undertaken to identify in-country epidemiological links. Combining WGS results for the isolates (all members of the central Asian strain [CAS]/Delhi genotype), from both European countries, an average genetic distance of 80 single-nucleotide polymorphisms (SNPs) (maximum, 153 SNPs) was observed. The few pairs of isolates with confirmed epidemiological links, except for one pair, had a maximum distance of 12 SNPs. WGS divided this refugee cluster into several subclusters of patients from the same country of origin. Although the M. tuberculosis cases, mainly originating from African countries, shared the exact same VNTR profile, most were clearly distinguished by WGS. The average genetic distance in this specific VNTR cluster was 2 times greater than that in other VNTR clusters. Thus, identical VNTR profiles did not represent recent direct M. tuberculosis transmission for this group of patients. It appears that either these strains from Africa are extremely conserved genetically or there is ongoing transmission of this genotype among refugees on their long migration routes from Africa to Europe.

EVALUASI KERAGAMAN GENETIK IKAN KANCRA DENGAN MENGGUNAKAN MARKER Mt DNA D-loop DAN RANDOM AMPLIFIED POLYMORPHISM DNA (RAPD)

Variasi genetik ikan kancra yang dikoleksi dari daerah Kuningan (Pesawahan, Gandasoli, dan Ragawacana) dan Sumedang di Jawa Barat telah diteliti dengan menggunakan polimorfisme Mitokondria DNA D-loop dan Random Amplified Polymorphism DNA (RAPD). Berdasarkan analisis Mt DNA tidak terdapat perbedaan yang nyata antara ras ikan kancra dari empat lokasi tersebut. Sedangkan analisis RAPD menunjukkan perbedaan yang nyata. Panjang daerah Mt DNA D-loop ikan kancra berkisar antara 700--800 bp. Satu komposit haplotype terdeteksi dengan menggunakan 4 enzim restriksi yaitu Rsa I, Nde II, Taq I, dan Sac I pada sekuens D-loop. Dua dari 20 primer RAPD menunjukkan perbedaan yang nyata di antara keempat populasi ikan kancra. Jarak genetik berdasarkan polimorfisme dua primer tersebut adalah 0,349.The aim of this research was to evaluate genetic variability of Tor soro. The genetic variability of Tor soro collected from Kuningan (Pesawahan, Gandasoli, and Ragawacana) and Sumedang, West Java were examined using polymorphism of the mitochondria DNA (MtDNA) D-loop and RAPD markers. Based on MtDNA D-loop analysis, there was no significant different among collection. The length size of MtDNA D-loop region was approximately 700--800 bp. A composite haplotype was detected using four endonuclease i.e. Rsa I, Nde II, Taq I, and Sac I. Two of 20 RAPD primers showed significantly different among collections. Average genetic distance based on the polymorphism of two primers was 0.349.

EVALUASI VARIASI GENETIK TIGA RAS IKAN GURAME ( Osphronemus gouramy ) DENGAN MENGGUNAKAN ISOZYME

Evaluasi variasi genetik tiga ras ikan gurame dilakukan sebagai tahap awal dalam mengatasi masalah budi daya ikan gurame yaitu tumbuh lambat. Variasi genetik ras ikan gurame yaitu bastar, bule, dan blusafir yang dikoleksi dari daerah Parung-Bogor, Jawa Barat telah dievaluasi dengan menggunakan isozyme. Tidak terdapat perbedaan yang nyata di antara tiga ras ikan gurame yang diuji. Jumlah alel per lokus dan alel polymorfik berturut-turut berkisar 1,25—1,375 dan 25%--37,5%; sedangkan heterosigositas berkisar 0,125--0,137. Jarak genetik antara ras blusafir dengan bastar atau bule adalah lebih besar dibandingkan jarak genetik antara ras bastar dengan bule. Jarak genetik rata-rata di antara ketiga ras ikan gurame adalah 0,0003.Evaluation of genetic variability of three giant gouramy races is an initial effort to solve the problem in culturing giant gouramy i.e. low growth. Genetic variability of three giant gouramy races, i.e. bastar, bule, and blusafir collected from ParungBogor, West Java is evaluated using isozyme. There is no significant difference among three giant gouramy races. Number of allele per locus and polymorphism allele were ranged 1.25--1.375 and 25.0%--37.5% respectively, while heterozygosity was ranged 0.125--0.137. Genetic distance between blusafir and bastar or bule is farthest than genetic distance between bastar and bule. The average genetic distance among giant gouramy races is 0.0003.

Genetic Variability of two Fagus sylvatica (L.) Populations in the South-Western Edge of the Panonnian Plain

- Two beech populations at altitudes of 273 m (Vrhovo) and 657 m (Kozarje), growing on significantly different forest site, in different ecological conditions and with different forestmanagement history were selected on Gorjanci Mountains and genetically investigated by means of isoenzyme analysis. A cline from minor to major allelic polymorphism was revealed at gene loci Aco- B, Idh-A and 6-Pgdh-A. At locus Skdh-A, allele A4 was observed only at the lower altitude population Vrhovo as a heterozygote genotype Skdh-A34 (12%). The Kozarje population of beech had a slightly higher genetic multiplicity, a slightly higher effective number of alleles per locus, higher observed heterozygosity and a higher level of intrapopulation differentiation. Statistically significant differences in the occurrence of alleles between populations were found at 5 of 16 loci. The average genetic distance of Gregorius (1974) was 6.1%. European beech populations analyzed from different altitudes on Gorjanci Mountains appeared to be genetically differentiated. The results presented are also discussed in the light of the climate change impact on forests.

Molecular characterization of elephantgrass accessions through RAPD markers

Elephantgrass pastures are limited by yield variations and reductions in forage quality and availability, thus making the search for genotypes with reduced seasonality a major concern. In order to verify the extent of genetic variability among contrasting cultivars, ten elephantgrass accessions were analyzed through DNA amplification by RAPD technique. A total of 160 DNA bands were generated with the use of 44 random primers and 23% of these bands were monomorphic for all accessions. Gel-obtained binary data (1 for presence and 0 for absence) were used for generating a genetic distance matrix, which was utilized in a UPGMA grouping analysis. Elephantgrass cultivars Cameroon and Vruckwona were the accessions mostly divergent from the others, with an average genetic distance of 0.34. The accessions with the lowest average genetic distances from the others were Pioneiro and CNPGL 27-5, both with a distance of 0.25. Overall, genetic distances ranged from 0.06 to 0.43, indicating little genetic variability for the set of accessions, despite the contrasting morphology of the studied genotypes.