Moderate Genetic Differentiation Research Articles

Genetic Differentiation and Relationship among Castanopsis chinensis, C. qiongbeiensis, and C. glabrifolia (Fagaceae) as Revealed by Nuclear SSR Markers

Castanopsis chinensis (Spreng.) Hance is widespread in the subtropical forests of China. Castanopsis qiongbeiensis G.A. Fu and Castanopsis glabrifolia J. Q. Li & Li Chen are limited to the coastal beaches of Wenchang county in the northeast of Hainan Island, and have similar morphological characteristics to C. chinensis. It is supposed that C. qiongbeiensis and C. glabrifolia are closely related to C. chinensis. In the present study, the genetic differentiation, gene flow, and genetic relationship of C. chinensis, C. qiongbeiensis, and C. glabrifolia were investigated by using 15 nuclear microsatellite markers; a total of 308 individuals from 17 populations were sampled in the three species. The allelic variation of nuclear microsatellites revealed moderate but significant genetic differentiation (FCT = 0.076) among C. chinensis, C. qiongbeiensis, and C. glabrifolia, and genetic differentiation between C. chinensis and C. glabrifolia was larger than that between C. chinensis and C. qiongbeiensis. Demographic simulations revealed unidirectional gene flow from C. chinensis to C. glabrifolia and C. qiongbeiensis, which highlight dispersal from mainland to island. The isolation effect of Qiongzhou Strait increased the genetic differentiation of species on both sides of the strait; however, the differentiation was diminished by gene flow that occurred during the historical period when Hainan Island was connected to mainland China. Our results supported the argument that C. glabrifolia should be considered an independent species and argued that C. qiongbeiensis should be regarded as an incipient species and independent conservation unit.

Genetic structure of ten Artemia populations from China: cumulative effects of ancient geological events, climatic changes, and human activities

This study investigated the population genetics and distribution patterns of Artemia populations from ten inland salt lakes in China. A total of 1,274,698 Artemia single nucleotide polymorphisms (SNPs) were identified. The results showed that these populations could be geographically and genetically divided into four distinct groups, and that the Tibetan populations were further divided into two subpopulations with a trend of decreasing genetic diversity from west to east. The Tibetan population had the highest genetic diversity, whereas the Shanxi population had the lowest. There was moderate genetic differentiation between the Tibetan populations and greater genetic differentiation between the Xinjiang and Shanxi populations. IBD (isolation by distance) suggested that geographical isolation contributes to genetic differentiation. In addition, there was some degree of gene flow among the ten populations, with A. sinica showing unidirectional gene flow in all populations in the eastern Nagri region. Species distribution modeling showed that mean annual temperature, temperature seasonality, and annual precipitation were the main environmental factors affecting the distribution of Artemia populations and suitable habitats for Tibetan populations will be further reduced in the future. It is necessary to strengthen the protection of germplasm resources and formulate scientific protocols for the sustainable development and utilization of Artemia resources.

A foundation for comparative genomics and evolutionary studies in Nucella lapillus based on complete mitogenome assembly

The Atlantic dog whelk, Nucella lapillus, is a marine snail that exhibits divergent evolution in response to habitat adaptation, resulting in distinct populations at the phenotypic, genotypic, and karyotypic levels. In this study, we utilized short- and long-read NGS data to perform a de novo assembly of the entire mitochondrial genome of N. lapillus and developed a multiplex PCR protocol to sequence most of its length using ONT sequencing. Our analysis revealed a typical circular configuration of 16,474 bp in length with 13 protein-coding genes, 22 different tRNA genes, 2 of them showing two copies, 2 rRNA genes, and a control region. Long-read sequencing enabled us to identify a 1826 bp perfect inverted repeat within the control region. Comparative analysis of the mitogenomes of related species in the Muricidae family revealed a conserved gene configuration for N. lapillus. We found a low genetic diversity, as well as a moderate genetic differentiation among the studied populations. Interestingly, there was no observed differentiation between the two chromosomal races, suggesting either introgression and permanent incorporation of the mitochondrial DNA haplotype from one of the chromosomal races into the other or a slower evolutionary rate of the mtDNAs with respect to that of the karyotypes. Our study serves as a foundation for comparative genomics and evolutionary investigations in this species.

Genetic diversity, population structure and origin of the native goats in Central Laos.

Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (FST: 0.011-0.043) and negligible inbreeding coefficients (FIS: -0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92-6.85 Mb, with short ROH segments (1-5 Mb length) being the most prevalent (66.34%). Longer ROH segments (20-40 and >40 Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features.

Aromatic rice (Oryza sativa L.) landraces of Indo‐Gangetic Plains of India harbor rich genetic diversity

AbstractAromatic rice (Oryza sativa L.) germplasm conserved in global genebanks needs intensive characterization to assess genetic diversity and population structure for crop improvement. We analyzed a panel of 92 accessions of non‐Basmati aromatic rice landrace germplasm with 23 phenotypic traits and 48 microsatellite markers. The landrace accessions displayed a huge phenotypic diversity for traits, namely, culm length, flag‐leaf length, panicle‐bearing tillers (PBT), plant height, panicle length, peduncle length, panicle exsertion, grain length, grain width, hull color, and 1000‐grain weight (TGW). Phenotypic clustering revealed three major clusters and five principal components explained 81.24% of the variance. TGW was associated positively with grain length, grain width, peduncle length, and grain yield but negatively with culm length and PBT. A total of 528 microsatellite alleles were detected, with 11.0 alleles per locus, revealing the presence of high polymorphism. Genetically, four subpopulations were detected based on structure analysis. In the germplasm, high levels of gene flow (Nm = 1.51) and gene diversity (HE = 0.83) were found. Among the subpopulations, we discovered high levels of inbreeding (FIS = 0.92) and moderate genetic differentiation (FST = 0.14). High polymorphism information content (0.806) along with a high level of molecular variance among genotypes (79%) was detected. A large number of multiple alleles were detected in numerous landrace accessions, revealing the presence of heterogeneity and heterozygotes in the landrace germplasm. The results of the present study are vital for the utilization of landrace diversity in the genetic improvement programs designed for rice quality improvement and consumer preference.

Analysis of Genetic Diversity and Structure of Eight Populations of Nerita yoldii along the Coast of China Based on Mitochondrial COI Gene.

Nerita yoldii is a euryhaline species commonly found in the intertidal zone. To investigate the genetic diversity of 233 N. yoldii individuals from eight locations along the coast of China, we utilized the mitochondrial COI gene as a molecular marker. A total of 34 haplotypes were detected, exhibiting a mean haplotype diversity (Hd) of 0.5915 and a mean nucleotide diversity (Pi) of 0.0025, indicating high levels of genetic diversity among all populations. An analysis of molecular variance (AMOVA) indicated that the primary source of genetic variation occurs within populations. In addition, neutral tests and mismatch analyses suggested that N. yoldii populations may have experienced bottleneck events. Moderate genetic differentiation was observed between Xiapu and other populations, excluding the Taizhou population, and may be attributed to the ocean currents. Intensively studying the genetic variation and population structure of N. yoldii populations contributes to understanding the current population genetics of N. yoldii in the coastal regions of China. This not only provides a reference for the study of other organisms in the same region but also lays the foundation for the systematic evolution of the Neritidae family.

Deciphering the maternal ancestral lineage of Greek Cypriots, Armenian Cypriots and Maronite Cypriots.

Cyprus was conquered from several populations because of its special geographical location. In this study, 406 unrelated Cypriot samples were tested based on their mitochondrial DNA. In more detail, 185 were Greek Cypriots, 114 Armenian Cypriots and 107 Maronite Cypriots. This is the first time where the mitochondrial DNA of Greek Cypriots, Armenian Cypriots and Maronite Cypriots is compared with the aim of characterizing the maternal ancestry of Cypriots. The control region of the mtDNA is the most informative in terms of studying maternal ancestry and consists of three hypervariable regions (HVS-I, HVS-II, HVS-III). The hypervariable regions can provide important information regarding the maternal ancestor of the tested samples. The entire control region of the mtDNA was used to determine the mitotypes and subsequently the haplogroups of all the Cypriot DNA samples. Based on the aforementioned analyses, Greek Cypriots were found to be genetically closer to Armenian Cypriots, while Greek Cypriots and Armenian Cypriots showed moderate genetic differentiation with Maronite Cypriots. The most prevalent haplogroups among Cypriots were haplogroups H and U, while R0 is common but in different frequencies for Greek Cypriots, Armenian Cypriots and Maronite Cypriots. It is proposed that the maternal ancestor may have originated during the Neolithic period and/or the Bronze age.

Genetic Diversity, Population Structure and Selection Signature in Begait Goats Revealed by Whole-Genome Sequencing.

Goats belong to a group of animals called small ruminants and are critical sources of livelihood for rural people. Genomic sequencing can provide information ranging from basic knowledge about goat diversity and evolutionary processes that shape genomes to functional information about genes/genomic regions. In this study, we exploited a whole-genome sequencing data set to analyze the genetic diversity, population structure and selection signatures of 44 individuals belonging to 5 Ethiopian goat populations: 12 Aberegalle (AB), 5 Afar (AF), 11 Begait (BG), 12 Central highlands (CH) and 5 Meafure (MR) goats. Our results revealed the highest genetic diversity in the BG goat population compared to the other goat populations. The pairwise genetic differentiation (FST) among the populations varied and ranged from 0.011 to 0.182, with the closest pairwise value (0.003) observed between the AB and CH goats and a distant correlation (FST = 0.182) between the BG and AB goats, indicating low to moderate genetic differentiation. Phylogenetic tree, ADMIXTURE and principal component analyses revealed a classification of the five Ethiopian goat breeds in accordance with their geographic distribution. We also found three top genomic regions that were detected under selection on chromosomes 2, 5 and 13. Moreover, this study identified different candidate genes related to milk characteristics (GLYCAM1 and SRC), carcass (ZNF385B, BMP-7, PDE1B, PPP1R1A, FTO and MYOT) and adaptive and immune response genes (MAPK13, MAPK14, SCN7A, IL12A, EST1 DEFB116 and DEFB119). In conclusion, this information could be helpful for understanding the genetic diversity and population structure and selection scanning of these important indigenous goats for future genetic improvement and/or as an intervention mechanism.

Characteristic of allele pool of sheep of the southern meat breed using microsatellite markers

Purpose: to characterize the allele pool of sheep of the southern beef breed using microsatellites.Materials and methods. The biomaterial was ear’s plucks from 80 sheep of the southern meat breed, selected from the Ladozhsky Breeding Plant. 20 East Friesian sheep, 33 Dorset sheep and 63 Romanov sheep were used for comparison. Nine microsatellite loci (INRA005, SPS113, INRA23, MAF65, McM527, OarCP49, HSC, OarAE129, MAF214) were selected as DNA markers. Microsatellite variability was analyzed using the ABI3130x1 Genetic Analyzer. The results were processed in the GenAIEx 6.503 program, with the help of which the main indicators characterizing the state of the allele pool and genetic diversity were calculated.Results. Analysis of the population genetic parameters of sheep of the southern meat breed showed that the average number of alleles per locus (Na) and the effective number of alleles per locus (Ne) exceed the sample average by 1,72 and 0,58 alleles, respectively. The expected heterozygosity (He) was 0,766, while the observed heterozygosity (Ho) was 0,741. The coefficient of inbreeding (Fis) was 0,03. The analysis of the principal components, carried out for the studied breeds in the planes of the first and third principal components, did not fundamentally change the nature of the spatial clustering of the studied groups of sheep. Analysis of the principal coordinates, performed on the basis of calculation of pairwise Fst values, showed that the southern meat breed is located in the upper left quadrant and is isolated from other breeds. The values of the Fst indicator indicate that there is moderate genetic differentiation between the southern meat and dorset breeds (Fst=0,116), and significant genetic differentiation between the southern meat and romanov breeds (Fst=0,161).Conclusion. An analysis of the population genetic parameters of sheep of the southern meat breed, in comparison with the east friesian, dorset and romanov breeds, showed that, in general, in terms of the total number of alleles per locus and the number of effective alleles per locus, it is characterized by a high level of genetic diversity. The presence of a tendency towards a deficiency of heterozygotes is probably explained by the limited population, represented by the only relict gene pool in Russia.

Microsatellite Analysis of the Genetic Diversity of Mussels from the North-Western Region of the Black Sea

Using four microsatellite DNA markers (<i>Mch 5, Mch 8, MT 203, MT 282</i>), the genetic diversity and population structure of three groups of mussels from the north-western section of the Black Sea were analyzed, and mussels from the Baltic and North Seas were studied as outgroups. By the studied microsatellite (MS) loci, 59 alleles were determined in five mussels' groups (<i>n</i> = 118). The observed heterozygosity (<i>H<sub>O</sub></i>) ranged from 0.083 to 0.538 and was lower than expected (<i>H<sub>E</sub></i> = 0.344-0.858). All mussel groups showed heterozygote deficiency, which suggests the possibility of inbreeding. Weak (<i>F<sub>ST</sub></i> = 0.036-0.048) and moderate (<i>F<sub>ST</sub></i> = 0.054-0.127) genetic differentiation between the studied groups of mussels was revealed. Genetic distances between the mussels' groups from different locations were calculated, which ranged from 0.211 to 1.130. The obtained data were confirmed by cluster and coordinate analyzes carried out using genetic distances between the groups by distribution of alleles frequencies.

Population genetics analysis of the black rockfish Sebastes schlegelii in Northern China based on 2b-RAD simplified genome sequencing

The black rockfish Sebastes schlegelii is an important fishery species in Japan, South Korea, and China. Overfishing has severely depleted the natural resources of S. schlegelii in recent years, leading to the initiation of programs aimed at enhancing fish stock. However, the genetic structure of northern populations remains elusive, posing challenges in collecting and preserving germplasm resources. In this study, a total of 191 S. schlegelii individuals from seven populations, including one cultured population (Changdao: CDYZ) and six wild populations (Lianyungang: LYG; Qingdao: QD; Weihai: WH; Changdao: CDYS; Beidaihe: BDH) sequenced by 2b-RAD method and their population genetics was analyzed using 27,064 SNPs obtained. The results indicated low genetic diversity in both wild and cultured populations (PIC < 0.25, Ho: 0.174-0.273, He: 0.173-0.234), with the cultured population exhibiting higher diversity than the wild ones. Moderate genetic differentiation existed between the cultured population and six wild populations (0.05 < Fst < 0.25). However, the genetic differentiation was lower among the other wild populations (Fst < 0.05). The analyses of population genetic structure indicated that the wild populations clustered together first and finally with the cultured population CDYZ, which clustered separately except for one individual. Therefore, scientific breeding programs and germplasm conservation can be important in stabilizing genetic structure. In addition, gene flow among the seven populations was high (Nm > 1). This study provides a theoretical basis for conserving and rationalizing germplasm resources for S. schlegelii.

Genetic diversity and divergence among native and translocated populations of the golden flathead goby Glossogobius aureus (Gobiiformes: Gobiidae) in Philippine lakes

The golden flathead goby Glossogobius aureus is a native species in the Philippines, Australia, Japan, Taiwan, and many other countries in Asia. In the Philippines, it is an important food fish as it is commonly caught in major lakes. In this study, a total of 307 specimens morphologically identified as G. aureus were sampled from nine major lakes in the Philippines and were sequenced for their mitochondrial cytochrome b (cyt b) gene. Two hundred sixty of the 307 cyt b sequences had sequence similarities of ≥ 99% with G. aureus reference sequence in GenBank, while the remaining 47 (all from Lake Lanao) had sequence similarities of only 95% and were thus designated as Glossogobius cf. aureus and treated as a separate population. The sequences were then analyzed to examine the pattern of genetic diversity, relatedness, divergence, and demographic history among native and translocated populations of the species. Twenty-nine haplotypes were recovered, of which four haplotypes were shared among three to seven populations. Only one haplotype each was found in the native population in Lake Buhi and translocated population in Lake Paoay. Low haplotype and low nucleotide diversities were found for the populations in Laguna de Bay, Lanao, Bato, Buhi, Paoay, and Sebu lakes, which indicate founder event for the introduced populations in Lanao, Paoay, and Sebu lakes and recent genetic bottleneck for the native populations in Laguna de Bay, Bato, and Buhi. In contrast, high haplotype but low nucleotide diversities were found for the native populations of Taal, Naujan, and Buluan lakes, signifying a recent bottleneck followed by population expansion. Pairwise FST values showed generally large (FST = 0.168–0.249) to very large (FST = 0.302–1.000) genetic divergence between populations except between Laguna de Bay and Lake Bato, Laguna de Bay and Lake Buhi, and Lake Bato and Lake Buhi populations, which showed nonsignificant genetic differentiation. Lake Buluan and Lake Sebu populations showed moderate genetic differentiation (FST = 0.098). Neutrality tests showed significant negative Tajima’s D and Fu’s FS values only for the population from Laguna de Bay, which suggests that the population is undergoing expansion. These results are important for establishing scientifically sound strategies for effective conservation and sustainable exploitation of G. aureus in the Philippines.

Genetic diversity, variation, and structure of two populations of bigfin reef squid (Sepioteuthis lessoniana d’Orbigny) in Con Dao and Phu Quoc islands, Vietnam

BackgroundBigfin squid is one of the economically important seafood resources in Vietnam’s fisheries and the waters around Con Dao and Phu Quoc islands are two major fishing grounds where this species has been actively exploited. The start codon targeted polymorphism (SCoT) and CAAT box–derived polymorphism (CBDP) techniques were used to generate DNA fingerprinting data to analyze the genetic diversity, variation, and structure of the two populations in the waters surrounding Phu Quoc and Con Dao islands together with mitochondrial cytochrome C oxidase subunit I (COI) gene sequence data. ResultsCon Dao population possessed a higher diversity [expected heterozygosity (He) = 0.2254, Shannon index (I) = 0.3459, percentage of polymorphic bands (PPB) = 80.14%, nucleotide diversity (π) = 0.0336, haplotype diversity (h) = 0.910 with 16 haplotypes] than Phu Quoc population (He = 0.1854, I = 0.2873, PPB = 70.38%, π = 0.0246, h = 0.838 with 14 haplotypes). The genetic diversity at species level in the investigated region was at level of He = 0.2169, I = 0.3399, PPB = 86.41, π = 0.0289, and h = 0.892 with 24 haplotypes. Based on DNA fingerprinting data, the pairwise genetic similarity coefficients among individuals of the Con Dao population were lower (average of 0.7977) than the Phu Quoc population (average of 0.8316). Based on mitochondrial COI data, the pairwise genetic distances among individuals of the Con Dao population were higher (average of 0.0361) than the Phu Quoc population (average of 0.0263). Gene differentiation (GST) between two investigated populations was 0.0316 and 0.0310 leading to the genetic distance was 0.0573 and 0.0213 and the gene flow between them was Nm = 8.2209 and 11.4700 migrants per generation among populations based on DNA fingerprinting and based on COI gene sequence data, respectively. Genetic variation within individuals of both populations (WP) played the key role in total genetic variation at species level in surveyed region. ConclusionsFor the bigfin reef squid species in the surveyed region, the Con Dao population had the higher genetic diversity than the Phu Quoc population, between them existed a low to moderate genetic differentiation and a genetic exchange via gene flow. The DNA fingerprinting data better revealed the genetic differentiation between the two surveyed populations while the mitochondrial COI gene sequence data could show the phylogenetic relationship among the surveyed individuals and the other from the sea regions in Southeast Asia. Based on the results obtained, fisheries management strategies are suggested toward the conservation and sustainable exploitation of this species.

Genetic variability of wild palms Euterpe precatoria, Euterpe oleracea and Mauritia flexuosa with molecular markers ISSR

Wild palms constitute a group of plants of particular economic importance in the tropics, being a valuable source for obtaining construction materials, fabrics, fuel, food, ornamental and medicinal plants. Despite their economic, social, and environmental importance, the genetic variability existing in wild palms, mainly of the genus Mauritia and Euterpe, is unknown, which limits their potential use and the identification of promising genotypes to be included in recombination programs. The genetic variability of three wild palm species (Euterpe oleracea, Euterpe precatoria, and Mauritia flexuosa) was evaluated using Inter-Simple Sequence Repeat (ISSR) markers. A total of 51 genotypes were analyzed with seven ISSR primers, which generated a total of 153 bands, with a percentage of polymorphic loci of 90.24%. The cluster analysis revealed the formation of six groups at a similarity level of 37%, grouping the palm genotypes by species and geographical origin. Molecular variance analysis revealed that within group variations contributed more to genetic diversity (89%) than between group variations (11%). The average value of Fst was 0.20, demonstrating moderate genetic differentiation. The high genetic variability found in this study indicates the valuable genetic potential present in palm germplasm, which could be used for future improvement programs of the species.

The Breeding Pattern and Population Genetic Structure of Coptotermes gestroi (Blattodea: Rhinotermitidae) Population in Natural Woodland Habitats

Microsatellite markers are suitable tools for assessing the population structure of eusocial species, especially those with a dynamic breeding system, such as the Asian subterranean termite Coptotermes gestroi (Wasmann) (Blattodea: Rhinotermitidae). Therefore, this study applied seven microsatellite markers to infer the breeding pattern and population genetic structure of C. gestroi found in natural woodland habitats at Universiti Sains Malaysia, Penang, Malaysia. The natural woodland habitat C. gestroi colonies show significant deviation from HWE (all p < 0.05). The uncovered genetic pattern suggested that the C. gestroi colonies presented a combined breeding pattern of mixed- and extended-family colonies with moderate genetic differentiation and elevated inbreeding. In particular, the breeding pattern of C. gestroi colonies was inferred to vary depending on the demographic variation and the age of the colony. Nevertheless, the results revealed comprehensive information on the C. gestroi population structure, habitat-specific to natural woodlands. Furthermore, future studies with exclusive datasets on the population structure of C. gestroi on marginal demography are necessary to enhance the management strategies of this pest species.

Postglacial phylogeography, admixture, and evolution of red spruce (Picea rubens Sarg.) in Eastern North America.

Climate change is a major evolutionary force that can affect the structure of forest ecosystems worldwide. Red spruce (Picea rubens Sarg.) has recently faced a considerable decline in the Southern Appalachians due to rapid environmental change, which includes historical land use, and atmospheric pollution. In the northern part of its range, red spruce is sympatric with closely related black spruce (Picea mariana (Mill.) B.S.P.), where introgressive hybridization commonly occurs. We investigated range-wide population genetic diversity and structure and inferred postglacial migration patterns and evolution of red spruce using nuclear microsatellites. Moderate genetic diversity and differentiation were observed in red spruce. Genetic distance, maximum likelihood and Bayesian analyses identified two distinct population clusters: southern glacial populations, and the evolutionarily younger northern populations. Approximate Bayesian computation suggests that patterns of admixture are the result of divergence of red spruce and black spruce from a common ancestor and then introgressive hybridization during post-glacial migration. Genetic diversity, effective population size (Ne) and genetic differentiation were higher in the northern than in the southern populations. Our results along with previously available fossil data suggest that Picea rubens and Picea mariana occupied separate southern refugia during the last glaciation. After initial expansion in the early Holocene, these two species faced a period of recession and formed a secondary coastal refugium, where introgressive hybridization occurred, and then both species migrated northward. As a result, various levels of black spruce alleles are present in the sympatric red spruce populations. Allopatric populations of P. rubens and P. mariana have many species-specific alleles and much fewer alleles from common ancestry. The pure southern red spruce populations may become critically endangered under projected climate change conditions as their ecological niche may disappear.

Cross species/genera transferability of simple sequence repeat markers, genetic diversity and population structure analysis in gladiolus (Gladiolus × grandiflorus L.) genotypes.

Genetic analysis of gladiolus germplasm using simple sequence repeat (SSR) markers is largely missing due to scarce genomic information. Hence, microsatellites identified for related genera or species may be utilized to understand the genetic diversity and assess genetic relationships among cultivated gladiolus varieties. In the present investigation, we screened 26 genomic SSRs (Gladiolus palustris, Crocus sativus, Herbertia zebrina, Sysirinchium micranthum), 14 chloroplast SSRs (Gladiolus spp., chloroplast DNA regions) and 25 Iris Expressed Sequence Tags (ESTs) derived SSRs across the 84 gladiolus (Gladiolus × grandiflorus L.) genotypes. Polymorphic markers detected from amplified SSRs were used to calculate genetic diversity estimates, analyze population structure, cluster analysis and principal coordinate analysis (PCoA). A total of 41 SSRs showed reproducible amplification pattern among the selected gladiolus cultivars. Among these, 17 highly polymorphic SSRs revealed a total of 58 polymorphic alleles ranging from two to six with an average of 3.41 alleles per marker. Polymorphic information content (PIC) values ranged from 0.11 to 0.71 with an average value of 0.48. A total of 4 SSRs were selectively neutral based on the Ewens-Watterson test. Hence, 66.66% of Gladiolus palustris, 48% of Iris spp. EST, 71.42% of Crocus sativus SSRs showed cross-transferability among the gladiolus genotypes. Analysis of genetic structure of 84 gladiolus genotypes revealed two subpopulations; 35 genotypes were assigned to subpopulation 1, 37 to subpopulation 2 and the remaining 12 genotypes could not be attributed to either subpopulation. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations, whereas 36.55% of variation among individuals within the total population. The least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation between two subpopulations was observed. The grouping pattern of population structure was consistent with the unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on simple matching dissimilarity coefficient and PCoA. SSR markers from the present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement. Genetic relationships assessed among the genotypes of respective clusters may assist the breeders in selecting desirable parents for crossing.

Analysis of global Napier grass (Cenchrus purpureus) collections reveals high genetic diversity among genotypes with some redundancy between collections

Genetic diversity amongst genotypes of several Napier grass collections was analyzed and compared with the diversity in a set of open pollinated progeny plants. A total of 114,881 SNP and 46,293 SilicoDArT genome-wide markers were generated on 574 Napier grass genotypes. Of these, 86% of the SNP and 66% of the SilicoDArT markers were mapped onto the fourteen chromosomes of the Napier grass genome. For genetic diversity analysis, a subset of highly polymorphic and informative SNP markers was filtered using genomic position information, a maximum of 10% missing values, a minimum minor allele frequency of 5%, and a maximum linkage-disequilibrium value of 0.5. Extensive genetic variation, with an average Nei’s genetic distance value of 0.23, was identified in the material. The genotypes clustered into three major and eleven sub-clusters with high levels of genetic variation contained both within (54%) and between (46%) clusters. However, we found that there was low to moderate genetic differentiation among the collections and that some overlap and redundancy occurred between collections. The progeny plants were genetically diverse and divergent from the germplasm collections, with an average FST value of 0.08. We also reported QTL regions associated with forage biomass yield based on field phenotype data measured on a subset of the Napier grass collections. The findings of this study offer useful information for Napier grass breeding strategies, enhancement of genetic diversity, and provide a guide for the management and conservation of the collections.

Contrasting patterns of genetic diversity and population discontinuity in the common red seaweed Gracilaria salicornia (Gracilariaceae) along the coasts of Thailand

ABSTRACT For long-term management and conservation of marine resources an understanding of their genetic diversity and geographic distribution is necessary. The red alga Gracilaria salicornia is widely distributed along the coasts of Thailand and has been used as food and as fertilizer. However, there have been no studies examining the genetic diversity of this alga. The present research aimed to employ two different genetic markers, mitochondrial (COI-5P) and chloroplast (RuBisCO spacer) for exploring the genetic diversity and phylogeography of G. salicornia in Thailand. Our analyses, inferred from both markers, revealed different levels of genetic diversity between the two coasts of Thailand, and the recognition of seven new COI haplotypes. Gracilaria salicornia in the Andaman Sea had higher genetic diversity than in the Gulf of Thailand. Significant genetic divergence was found between populations in the Andaman Sea and the Gulf of Thailand, likely due to the geographic barrier of the Thai-Malay Peninsula and the complex ocean currents. No genetic structuring was detected in the Gulf of Thailand, whereas low to moderate genetic differentiation was found between populations in the Andaman Sea, suggesting a possible break between the northern and southern Andaman Sea. This break could be explained by ocean circulation patterns around the Malacca Strait. These findings provide further evidence supporting the Thai-Malay Peninsula and oceanographic currents as strong barriers to dispersal, leading to genetic differentiation and population structuring of G. salicornia and other marine species. These results can be used to guide conservation management actions and exploitation of this marine resource.

Genetic differentiation among Aedes aegypti populations from different eco-geographical zones of India.

The present study explicitly evaluated the genetic structure of Aedes aegypti Linn, the vector of dengue, chikungunya, and Zika viruses, across different geo-climatic zones of India and also elucidated the impact of ecological and topographic factors. After data quality checks and removal of samples with excess null alleles, the final analysis was performed on 589 individual samples using 10 microsatellite markers. Overall findings of this study suggested that, Ae. aegypti populations are highly diverse with moderate genetic differentiation between them. Around half of the populations (13 out of 22) formed two genetic clusters roughly associated with geographical regions. The remaining nine populations shared genetic ancestries with either one or both of the clusters. A significant relationship between genetic and geographic distance was observed, indicating isolation by distance. However, spatial autocorrelation analysis predicted the signs of long-distance admixture. Post-hoc environmental association analysis showed that 52.7% of genetic variations were explained by a combination of climatic and topographic factors, with latitude and temperature being the best predictors. This study indicated that though overall genetic differentiation among Ae. aegypti populations across India is moderate (Fst = 0.099), the differences between the populations are developing due to the factors associated with geographic locations. This study improves the understanding of the Ae. aegypti population structure in India that may assist in predicting mosquito movements across the geo-climatic zones, enabling effective control strategies and assessing the risk of disease transmission.