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Genetic admixture and population structure analysis of Indian water buffaloes (Bubalus bubalis) using STR markers

We generated genetic diversity data for 10 different buffalo populations of India using 20 highly polymorphic microsatellite markers. The buffalo populations of Odisha were the primary focus, viz. Chilika, Paralakhemundi, Kalahandi, Sambhalpuri, and Manda. The total observed number of alleles ranged between 143 (Manda) and 301 (Paralakhemundi) with an average of 204 alleles per breed. The minimal spanning network based on Bruvo's distance, PCA based on the Fst values, and genetic admixture analysis using both the STRUCTURE and 'snapclust' could identify the Manda population distinct from other Odisha buffalo breeds as well as Chhattisgarhi buffalo breed. The Sambhalpuri buffalo population also clustered into two separate subpopulations, half of the unique sub-population located geographically south-wards displayed no admixture with any of the adjacent buffalo populations. The Sambhalpuri population requires elaborate analysis to confirm the existence of two distinct sub-populations and if they could be recognized as separate breeds. The limited number of sires in the Manda population has resulted in excess of heterozygosity. Furthermore, the Manda population is left with very little allelic richness and this poses a huge threat to the population's existence. In another way, the study has led to the identification of the Manda buffalo as a distinct population, and the germplasm has been registered based on the study.

The genetic architectures of vine and skin maturity in tetraploid potato

Potato vine and skin maturity, which refer to foliar senescence and adherence of the tuber periderm, respectively, are both important to production and therefore breeding. Our objective was to investigate the genetic architectures of these traits in a genome-wide association panel of 586 genotypes, and through joint linkage mapping in a half-diallel subset (N = 397). Skin maturity was measured by image analysis after mechanized harvest 120 days after planting. To correct for the influence of vine maturity on skin maturity under these conditions, the former was used as a covariate in the analysis. The genomic heritability based on a 10K SNP array was 0.33 for skin maturity vs. 0.46 for vine maturity. Only minor QTL were detected for skin maturity, the largest being on chromosome 9 and explaining 8% of the variation. As in many previous studies, S. tuberosum Cycling DOF Factor 1 (CDF1) had a large influence on vine maturity, explaining 33% of the variation in the panel as a bi-allelic SNP and 44% in the half-diallel as a multi-allelic QTL. From the estimated effects of the parental haplotypes in the half-diallel and prior knowledge of the allelic series for CDF1, the CDF1 allele for each haplotype was predicted and ultimately confirmed through whole-genome sequencing. The ability to connect statistical alleles from QTL models with biological alleles based on DNA sequencing represents a new milestone in genomics-assisted breeding for tetraploid species.

Spatial pattern of genetic diversity in field populations of Fusarium incarnatum-equiseti species complex

Fusarium is associated with a number of wilt, blight, scab and rot diseases in a range of economically important staple food crops worldwide. An assessment of the genetic structure and population stratification of Fusarium incarnatum-equiseti species complex (FIESC) pathogen populations is important to understand the evolutionary potential of such populations in adapting to environmental change. Based on inter-simple sequence repeat polymerase chain reaction (ISSR-PCR), it was found that the pathogen population was structured into three genetic clusters for which genetic differentiation was higher within than among populations. There was high intra-population genetic diversity for population 1 (94.63%) which consisted largely of isolates collected from North Trinidad. Populations 2 and 3 had a low level of admixture among the populations based on overall population differentiation. Population 1 accounted for the highest amount of genetic variation (95.82%) followed by populations 2 and 3. Population stratification was reflected in the dendrogram topology, which consisted of three main genetic clusters and which coincided with the outcome of Bayesian and PCoA analyses. The populations were isolated by distance and Voronoi tessellations indicated physical or structural barriers to gene flow which contributed to restricted admixture between two of three populations. These findings suggest a high evolutionary potential for this FIESC pathogen population, the implications of which directly affect disease management strategies.

opennotspecifiedJul 2018View details →

Distribution. SE Guinea, E Liberia, and SW Ivory Coast in West Africa; the species may be found in Sierra Leone, but this population has not been genetically investigated and could be either the Ivory Coast White-toothed Shrew or the West African Pygmy White-toothed Shrew (C. obscurior). in Soricidae

Distribution. SE Guinea, E Liberia, and SW Ivory Coast in West Africa; the species may be found in Sierra Leone, but this population has not been genetically investigated and could be either the Ivory Coast White-toothed Shrew or the West African Pygmy White-toothed Shrew (C. obscurior).

opennotspecifiedJul 2018View details →

Distribution. SE Guinea, E Liberia, S Ivory Coast, and W Ghana; populations ofeither this species, the Ivory Coast White-toothed Shrew (C. eburnea), or both species are found in S Sierra Leone and are included in the range map ofthis species but have not been investigated genetically and could represent either species. There are apparently records that represent this species from S Nigeria, although further research is needed to confirm thatthis speciesis truly found there. in Soricidae

Distribution. SE Guinea, E Liberia, S Ivory Coast, and W Ghana; populations ofeither this species, the Ivory Coast White-toothed Shrew (C. eburnea), or both species are found in S Sierra Leone and are included in the range map ofthis species but have not been investigated genetically and could represent either species. There are apparently records that represent this species from S Nigeria, although further research is needed to confirm thatthis speciesis truly found there.

opennotspecifiedJul 2018View details →

Distribution. Known definitely from two areas in N &W Sumatra (Mt Tujuh and Bukit Lawan), but if morphologically and genetically similar specimens from Borneo and Peninsular Malaysia prove to be conspecifics, its distribution might be more extensive across the Sundaland. in Soricidae

Distribution. Known definitely from two areas in N &W Sumatra (Mt Tujuh and Bukit Lawan), but if morphologically and genetically similar specimens from Borneo and Peninsular Malaysia prove to be conspecifics, its distribution might be more extensive across the Sundaland.

opennotspecifiedNov 2017View details →

Distribution. Based on molecular vouchers it occurs in E Zambia, Malawi, and Tanzania; records from N Mozambique, Zimbabwe, and N South Africa lack genetic verification, but are included here. in Muridae

Distribution. Based on molecular vouchers it occurs in E Zambia, Malawi, and Tanzania; records from N Mozambique, Zimbabwe, and N South Africa lack genetic verification, but are included here.

opennotspecifiedNov 2017View details →

Although previously included in O. typus, O. jackson: differs from it in body size, number of M® lamina, and genetically. Monotypic. Distribution. Known only from Mt Elgon, E Uganda and W Kenya. Descriptive notes. Head-body 120-171 mm, tail 57-82 mm, ear 19-26 mm, hindfoot 19-26 mm; weight 70-121 g. The Mount Elgon Vlei Rat is medium to large in size and robust, with large blunt head, shorttail, and shaggy fur; it is the smallest of the O. typus species group. Fur coloris not clearly distinct from the Ethiopian Vlei Rat (O. typus). Lower incisors each have two deep grooves. M, has four laminae, and M? has seven laminae. in Muridae

Although previously included in O. typus, O. jackson: differs from it in body size, number of M® lamina, and genetically. Monotypic. Distribution. Known only from Mt Elgon, E Uganda and W Kenya. Descriptive notes. Head-body 120-171 mm, tail 57-82 mm, ear 19-26 mm, hindfoot 19-26 mm; weight 70-121 g. The Mount Elgon Vlei Rat is medium to large in size and robust, with large blunt head, shorttail, and shaggy fur; it is the smallest of the O. typus species group. Fur coloris not clearly distinct from the Ethiopian Vlei Rat (O. typus). Lower incisors each have two deep grooves. M, has four laminae, and M? has seven laminae.

opennotspecifiedNov 2017View details →

Lophuromys stanley: is member of the L. flavopunctatus species complex and was named during partial revision of the L. aguilus species complex. It is characterized by craniometric and genetic character-istics; its skull proportions are similar to L. laticeps, and molecularly, it is similar to L. margarettae and L. zena (cytochrome-b). Lophuromys stanleyi is one of four endemic species in the Rwenzori Mountains diversity hotspot. Monotypic. Distribution. Rwenzori Mts, E DR Congo and SW Uganda. Descriptive notes. Head-body 113-126 mm, tail 40-80 mm, ear 16-19 mm, hindfoot 22-24 mm; weight 36-55 g. The Rwenzori Brush-furred Rat has a speckled pelage similar to other speciesin the L. flavopunctatus species complex. Tail is short, 50-60% of head-body length. Habitat. Poorly known, but type specimen was collected at an elevation of 3700 m. Food and Feeding. No information. Breeding. No information. Activity patterns. No information. in Muridae

Lophuromys stanley: is member of the L. flavopunctatus species complex and was named during partial revision of the L. aguilus species complex. It is characterized by craniometric and genetic character-istics; its skull proportions are similar to L. laticeps, and molecularly, it is similar to L. margarettae and L. zena (cytochrome-b). Lophuromys stanleyi is one of four endemic species in the Rwenzori Mountains diversity hotspot. Monotypic. Distribution. Rwenzori Mts, E DR Congo and SW Uganda. Descriptive notes. Head-body 113-126 mm, tail 40-80 mm, ear 16-19 mm, hindfoot 22-24 mm; weight 36-55 g. The Rwenzori Brush-furred Rat has a speckled pelage similar to other speciesin the L. flavopunctatus species complex. Tail is short, 50-60% of head-body length. Habitat. Poorly known, but type specimen was collected at an elevation of 3700 m. Food and Feeding. No information. Breeding. No information. Activity patterns. No information.

Data from: Genetic dissection of grain iron and zinc, and thousand kernel weight in wheat (Triticum aestivum L.) using genome-wide association study

The study material in GWAS panel with 280 common bread wheat genotypes was selected from All India Coordinated Research Project on Wheat and Barley to map the genomic regions responsible for enhanced Grain Zinc Content (GZnC), Grain Iron Content (GZnC) and Thousand Kernel weight (TKW). Phenotypic data: The GWAS panel was evaluated at five different environments: E1-University of Agricultural Sciences, research farm, Dharwad (15°29'20.71"N, 74°59'3.35"E, 750m AMSL), E2-ICAR- Indian Agricultural Research Institute, New Delhi (28°38′30.5″N, 77°09′58.2″E, 228 m AMSL), E3-Indian Agricultural Research Institute, Jharkhand (24°16'58.4"N, 85°21'16.1"E, 651m AMSL), E4-ICAR-Indian Institute of Wheat and Barley, Karnal (29°41'8.2644''N, 76°59'25.9692''E, 250m AMSL), and E5-Punjab Agricultural University, Ludhiana (30o54' N, 75o48'E, 247m AMSL). Around 20 g of grain sample from each genotype were used for phenotyping GFeC and GZnC through high-throughput Energy Dispersive X-ray Fluorescence (ED-XRF) machine (model X-Supreme 8000; Oxford Instruments plc, Abingdon, United Kingdom) calibrated with glass beads-based values. To record TKW, the Numigral grain counter was used to count the grain number, the reading was set at 1000 grains and the weight of the grains was recorded in grams with an electronic balance. The GFeC, GZnC were expressed as milligram per kilogram (mg/kg), GPC in percentage (%), TKW in grams (gms). Genotypic data: Genomic DNA of the GWAS panel was extracted from the leaves of 21 days-old seedlings by Cetyl Trimethyl Ammonium Bromide (CTAB) method. The panel was genotyped using Axiom Wheat Breeder's Genotyping Array (Affymetrix, Santa Clara, CA, United States) having 35,143 genome-wide SNPs. The monomorphic, markers with minor allele frequency (MAF) of <5%, missing data of >20%, and heterozygote frequency >25% were removed from the analysis. The remaining set of 14,790 high-quality SNPs was used in GWAS analysis. The detailed information of the methods and software used, data analysis and GWAS is available at DOI: 10.1038/s41598-022-15992-z.

Spatio-temporal dynamics of genetic variation at the quantitative and molecular levels within a natural Arabidopsis thaliana population

Evolutionary change begins at the population scale. Therefore, understanding adaptive variation requires the identification of the factors maintaining and shaping standing genetic variation at the within-population level. Spatial and temporal environmental heterogeneity represent ecological drivers of within-population genetic variation, determining the evolutionary trajectory of populations along with random processes. Here, we focused on the effects of spatio-temporal heterogeneity on quantitative and molecular variation in a natural population of the annual plant Arabidopsis thaliana. We sampled 1,093 individuals from a Spanish A. thaliana population across an area of 7.4 ha for 10 years (2012-2021). Based on a sample of 279 maternal lines, we estimated spatio-temporal variation in life-history traits and fitness from a common garden experiment. We genotyped 884 individuals with nuclear microsatellites to estimate spatio-temporal variation in genetic diversity. We assessed spatial patterns by estimating spatial autocorrelation of traits and fine-scale genetic structure. We analyzed the relationships between phenotypic variation, geographic location and genetic relatedness, as well as the effects of environmental suitability and genetic rarity on phenotypic variation. The common garden experiment indicated that there was more temporal than spatial variation in life-history traits and fitness. Despite the differences among years, genetic distance in ecologically relevant traits (e.g. flowering time) tended to be positively correlated to genetic distance among maternal lines, whilst isolation by distance was less important. Genetic diversity exhibited significant spatial structure at short distances, which were consistent among years. Finally, genetic rarity, and not environmental suitability, accounted for genetic variation in life-history traits. Synthesis. Our study highlighted the importance of repeated sampling to detect the large amount of genetic diversity at the quantitative and molecular levels that a single A. thaliana population can harbor. Overall, population genetic attributes estimated from our long-term monitoring scheme (genetic relatedness and genetic rarity), rather than biological (dispersal) or ecological (vegetation types and environmental suitability) factors, emerged as the most important drivers of within-population structure of phenotypic variation in A. thaliana.

Is species richness mediated by functional and genetic divergence? A global analysis in birds

Unravelling why species richness varies shows such dramatic spatial variation is an ongoing challenge. Common to many theories is that increasing species richness requires a compensatory trade-off on an axis of species' ecology. Spatial variation in species richness may also affect genetic diversity if large numbers of coexisting, related species result in smaller population sizes. Here, we test whether increasing species richness results in differential occupation of morphospace by the constituent species, or decreases species' genetic diversity. We test for two potential mechanisms of morphological accommodation: denser packing in ecomorphological space, and expansion of the space. We then test whether species differ in their nucleotide diversity depending on allopatry or sympatry with relatives, indicative of potential genetic consequences of coexistence that would reduce genetic diversity in sympatry. We ask these questions in a spatially explicit framework, using a global database of avian functional trait measurements in combination with >120,000 sequences downloaded from GenBank. We find that higher species richness within families is not systematically correlated with either packing in morphological space or overdispersion but, at the Class level, we find a general positive relationship between packing and species richness, but that packing is comparatively greater in tropical points relative to their species richness. We find limited evidence that geographical co-occurrence with closely related species or tropical distributions decreases nucleotide diversity of nuclear genes; however, this requires further analysis. Our results suggest that avian families can accumulate species regionally with minimal tradeoffs or cost, implying that external biotic factors do not limit species richness.

FIGURE 4 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers

FIGURE 4: WARD tree of SCoT data revealing species delimitation in the Delphinium sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida; sp14= D. oliverianum; sp15= D. flavum; sp16= D. trigonelloides; sp17= D. oliganthum; sp18= D. linarioides; sp19= D. paradoxum.

FIGURE. 3 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers

FIGURE. 3. Electrophoresis gel of studied ecotypes from DNA fragments produced by SCoT-15. sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida; sp14= D. oliverianum; sp15= D. flavum; sp16= D. trigonelloides; sp17= D. oliganthum; sp18= D. linarioides; sp19= D. paradoxum. L = Ladder 100 bp,

FIGURE 2 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers

FIGURE 2: PCA plot of morphological characters revealing species delimitation in the Delphinium species; sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida; sp14= D. oliverianum; sp15= D. flavum; sp16= D. trigonelloides; sp17= D. oliganthum; sp18= D. linarioides; sp19= D. paradoxum.

FIGURE. 1 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers

FIGURE. 1. Map of Iran shows the collection sites and provinces where Delphinium species were obtained for this study; sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida

FIGURE 9 in Genetic and morphological variation analyses of Glandirana rugosa with description of a new species (Anura, Ranidae)

FIGURE 9. Map of Japan showing our results and the conclusion. Upper left: distributional ranges of Glandirana reliquia sp. nov. (dotted area, closed circle = type locality) and G. rugosa (gray area). Lower right: the sites where we collected molecular samples of Glandirana reliquia sp. nov. (squares) and four mtDNA groups of G. rugosa (circles). Locality numbers correspond with those shown in the supplementary Table 1 deposited in Figshare (DOI: 10.6084/m9.figshare.20290599).

FIGURE 8 in Genetic and morphological variation analyses of Glandirana rugosa with description of a new species (Anura, Ranidae)

FIGURE 8. Advertisement call of Glandirana reliquia sp. nov. from Tokyo, Japan, recorded at an air temperature of 20.1°C, showing sonogram (top) and wave form (bottom).

FIGURE 6 in Genetic and morphological variation analyses of Glandirana rugosa with description of a new species (Anura, Ranidae)

FIGURE 6. Dorsal (A) and ventral (B) views of the whole body and ventral view of left hand (C) and foot (D) of the male holotype of Glandirana reliquia sp. nov. (KUHE 64088). Scale bar = 20 mm (A, B)/5 mm (C, D). A lateral view of a nearly topotypic male in life (AUEZ 0843: Kamogawa City, Chiba Prefecture) is shown as well (E).

FIGURE 7 in Genetic and morphological variation analyses of Glandirana rugosa with description of a new species (Anura, Ranidae)

FIGURE 7. Dorsal (A), lateral (B), and ventral (C) views and the oral disc (D) of a tadpole of Glandirana reliquia sp. nov. in stage 35 of Gosner (1960), collected on 9 May 2013 at Sendai City, Miyagi Pref., Japan. Scale bar = 10 mm.