Polymorphism Information Content Research Articles

Genetic diversity and population structure of a modified three-way tomato hybrids for determining fruit size traits

The assessment of genetic diversity and genetic structure of crops has a vital impact on the plant breeding program, including the characterization, use and conservation of genetic material. The genetic diversity and genetic structure of a set of 94 F3 tomato hybrids were assessed with 25 polymorphic SNP markers of quantitative trait loci (QTLs) underlying fruit size in tomatoes using Sequenom Mass ARRAY system. A total of 50 alleles were amplified and the average polymorphic information content (PIC) was 0.2220. Nei's genetic distance ranged from 0 to 0.62. Therefore, single nucleotide sequence (SNP) markers detected a significantly high degree of polymorphism in tomato hybrids. Cluster analysis using the unweighted pair group method with arithmetic mean methods (UPMA) indicated that the tomato hybrids studied are grouped into four main groups, which is to some extent consistent with the size, shape and number of locules of the tomatoes studied. Analysis of population structure with SNP markers revealed three subpopulations. Association mapping using 25 SNP markers detected 9 markers with a significant association with mean fruit weight, fruit length, fruit diameter, number of locules, and fruit shape index. The nine markers detected in this study are recommended for the tomato fruit size improvement breeding program.

Genetic diversity analysis of Inner Mongolia cashmere goats (Erlangshan subtype) based on whole genome re-sequencing

BackgroundInner Mongolia cashmere goat (IMCG), renowned for its superior cashmere quality, is a Chinese indigenous goat breed that has been developed through natural and artificial selection over a long period. However, recently, the genetic resources of IMCGs have been significantly threatened by the introduction of cosmopolitan goat breeds and the absence of adequate breed protection systems.ResultsIn order to assess the conservation effectiveness of IMCGs and efficiently preserve and utilize the purebred germplasm resources, this study analyzed the genetic diversity, kinship, family structure, and inbreeding of IMCGs utilizing resequencing data from 225 randomly selected individuals analyzed using the Plink (v.1.90), GCTA (v.1.94.1), and R (v.4.2.1) software. A total of 12,700,178 high-quality SNPs were selected through quality control from 34,248,064 SNP sites obtained from 225 individuals. The average minor allele frequency (MAF), polymorphic information content (PIC), and Shannon information index (SHI) were 0.253, 0.284, and 0.530, respectively. The average observed heterozygosity (Ho) and the average expected heterozygosity (He) were 0.355 and 0.351, respectively. The analysis of the identity by state distance matrix and genomic relationship matrix has shown that most individuals’ genetic distance and genetic relationship are far away, and the inbreeding coefficient is low. The family structure analysis identified 10 families among the 23 rams. A total of 14,109 runs of homozygosity (ROH) were identified in the 225 individuals, with an average ROH length of 1014.547 kb. The average inbreeding coefficient, calculated from ROH, was 0.026 for the overall population and 0.027 specifically among the 23 rams, indicating a low level of inbreeding within the conserved population.ConclusionsThe IMCGs exhibited moderate polymorphism and a low level of kinship with inbreeding occurring among a limited number of individuals. Simultaneously, it is necessary to prevent the loss of bloodline to guarantee the perpetuation of the IMCGs’ germplasm resources.

Genetic diversity and population structure of Uganda cassava germplasm.

Cassava (Manihot esculenta Crantz) holds significant economic importance globally. Evaluating a diverse range of germplasm based on molecular characteristics not only enhances its preservation but also supports its utilization in breeding programs. In this study, we assessed genetic diversity and population structure among 155 cassava genotypes from Uganda using 5247 single nucleotide polymorphism (SNP) markers. Genotyping by sequencing (GBS) was employed for SNP discovery and to evaluate genetic diversity and population structure using the ADMIXTURE software. The cassava accessions comprised two populations: 49 accessions from Ugandan lines and 106 accessions resulting from crosses between South American and Ugandan lines. The average call rate of 96% was utilized to assess marker polymorphism. Polymorphic information content values of the markers ranged from 0.1 to 0.5 with an average of 0.4 which was moderately high. The principal component analysis (PCA) showed that the first two components captured ~ 24.2% of the genetic variation. The average genetic diversity was 0.3. The analysis of molecular variance (AMOVA) indicated that 66.02% and 33.98% of the total genetic variation occurred within accessions and between sub-populations, respectively. Five sub-populations were identified based on ADMIXTURE structure analysis (K = 5). Neighbor-joining tree and hierarchical clustering tree revealed the presence of three different groups which were primarily based on the source of the genotypes. The results suggested that there was considerable genetic variation among the cassava genotypes which is useful in cassava improvement and conservation efforts.

Emerging Cases of Cat-Transmitted Sporotrichosis Driven by Sporothrix brasiliensis in Northeast Brazil.

Cat-transmitted sporotrichosis is caused by the emerging fungal pathogen Sporothrix brasiliensis and constitutes a significant public health issue that affects people living in resource-poor urban centers in Brazil. The lack of knowledge about transmission dynamics makes it difficult to propose public health policies to contain the advance of sporotrichosis. We describe the recent emergence of 1,176 cases of sporotrichosis in cats (2016 to 2021) in the metropolitan region of Recife, Brazil, leading to significant zoonotic transmission and an overwhelming occurrence of S. brasiliensis as the etiological agent. Most cases were from cats in the cities of Olinda (408/1,176; 34.70%), Jaboatão dos Guararapes (332/1,176; 28.23%), and Recife (237/1,176; 20.15%). Molecular typing using amplified fragment length polymorphism (EcoRI-GA/MseI-AG) revealed low polymorphic information content (PIC = 0.2499) and heterozygosity (H = 0.2928), typical of an outbreak scenario. Dendrogram and multivariate cluster analysis revealed that isolates from Pernambuco are closely related to Rio de Janeiro isolates. We report a substantial occurrence of MAT1-2 idiomorphs in the metropolitan region of Recife (0:60 ratio; χ2 = 60.000, P < 0.0001). The limited population differentiation and genetic diversity of the isolates from Pernambuco suggest a recent introduction, possibly via a founder effect, from the parental population in Rio de Janeiro. Our findings emphasize the critical importance of molecular surveillance of S. brasiliensis for outbreak response. A comprehensive one-health strategy is mandatory to control the spread of cat-transmitted sporotrichosis driven by S. brasiliensis, encompassing sanitary barriers, quick diagnosis, and treatment.

Association study of allelic variation identified at yield contributing loci in rice (Oryza sativa L.)

The knowledge of functionally characterized genes and linked markers that govern grain yield and its related traits were used to unravel the markers/genes that associate with diversity of yield traits in a panel 30 novel rice genotypes comprising of indica, japonica, aromatic, landraces, interspecific crosses (O.glaberrima/O.sativa) etc. The ANOVA showed significant differences (P=&lt;0.001) for all traits among the genotypes. Molecular analysis was done by employing 37 gene-specific markers targeting 24 yield governing genes in rice. Two markers viz., RM223(YLD) on chromosome 8 and GW004(GW2, LOC_Os02g14720) on chromosome 2 were identified as polymorphic. Average PIC (polymorphic information content) value for these primers was 0.37, suggesting the availability of accountable variability at these loci. Cluster analysis grouped the genotypes into three clusters. Marker-trait-association analysis revealed significant association of the marker GW004 with panicle length, plant height and filled grains in rice. Pearson correlation study also supported the molecular associations through significant phenotypic associations for trait pairs plant height and filled grains, panicle length and plant height. The phenotypic variance explained (R2%) by the marker across panicle length, plant height and filled grains was ≥15%, suggesting major role of the locus/gene in controlling respective traits. Thus, GW004 marker could be employed in breeding programs for simultaneous selection of three traits panicle length, plant height and filled grains. From the current study it can be concluded that allelic variation studies using novel genotypes can result in the identification of suitable donors along with trait associated markers for rice yield improvement.

PHYLOGENETIC STUDY OF TEN SPECIES FROM CENTAUREA (ASTERACEAE) IN DUHOK CITY, KURDISTAN REGION-IRAQ

The current research aimed to estimate the evolutionary relationships of ten Centaurea L. species growing naturally in the Duhok City, Kurdistan region of Iraq. The combing Start Codon Targeted (SCoT) markers with Internal Transcribed Spacer (ITS) gene region barcode were performed. To detect the DNA sequence variations and phylogenetic tree reconstruction, the Dice similarity matrix, the unweighted pair group method with arithmetic mean (UPGMA) clustering and Maximum Likelihood (ML) methods were applied. 104 polymorphic bands were scored with an average of 10.4. The Polymorphic Information Content (PIC) and Resolving Power (Rp) values ranged between (0.24 to 0.36) and 3.4 in primer (SCoT1) to 12 in primer (SCoT53) with an average of 0.319 and 5.74 respectively. The lowest similarity value was 0.52 between C. behen L. and C. solstitialis L., while the highest was 0.82 between C. balsamita and C. rigida. The reconstructed polytomous dendrogram was as follows: clade one; C. solstitialis L.; clade 2, C. balsamita Lam. and C. virgata Lam.; clade three subdivide into two subclades: C. iberica Trev. ex Spreng., C. hayalolepis Boiss., C. brugueriana (DC) Hand. Mazz. and C. gigantea Sch. Bip. Ex Boiss., C. regia Boiss., C. rigida Banks &amp; Sol., C. behen Lam. Furthermore, C. brugueriana (DC) Hand. Mazz., C. iberica Trev. ex Spreng, C. behen L., C. solstiotialis L. and C. balsamita Lam. were nested with National Center for Biotechnology Information (NCBI). In contrast, the remaining taxa were mixed with other closely related species. Thus, ScoT markers and ITS DNA barcode were considerably effective for investigating the evolutionary relationships of Centaurea taxa.

Genetic diversity and population structure of wheat landraces in Southern Winter Wheat Region of China

BackgroundWheat landraces are considered a valuable source of genetic diversity for breeding programs. It is useful to evaluate the genetic diversity in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection. In addition, constructing a core germplasm set that represents the genetic diversity of the entire variety set is of great significance for the efficient conservation and utilization of wheat landrace germplasms.ResultsTo understand the genetic diversity in wheat landrace, 2,023 accessions in the Jiangsu Provincial Crop Germplasm Resource Bank were used to explore the molecular diversity and population structure using the Illumina 15 K single nucleotide polymorphism (SNP) chip. These accessions were divided into five subpopulations based on population structure, principal coordinate and kinship analysis. A significant variation was found within and among the subpopulations based on the molecular variance analysis (AMOVA). Subpopulation 3 showed more genetic variability based on the different allelic patterns (Na, Ne and I). The M strategy as implemented in MStratv 4.1 software was used to construct the representative core collection. A core collection with a total of 311 accessions (15.37%) was selected from the entire landrace germplasm based on genotype and 12 different phenotypic traits. Compared to the initial landrace collections, the core collection displayed higher gene diversity (0.31) and polymorphism information content (PIC) (0.25), and represented almost all phenotypic variation.ConclusionsA core collection comprising 311 accessions containing 100% of the genetic variation in the initial population was developed. This collection provides a germplasm base for effective management, conservation, and utilization of the variation in the original set.

Genome-wide association study for cashmere traits in Inner Mongolia cashmere goat population reveals new candidate genes and haplotypes

BackgroundThe cashmere goat industry is one of the main pillars of animal husbandry in Inner Mongolia Autonomous Region, and plays an irreplaceable role in local economic development. With the change in feeding methods and environment, the cashmere produced by Inner Mongolia cashmere goats shows a tendency of coarser, and the cashmere yield can not meet the consumption demand of people. However, the genetic basis behind these changes is not fully understood. We measured cashmere traits, including cashmere yield (CY), cashmere diameter (CD), cashmere thickness (CT), and fleece length (FL) traits for four consecutive years, and utilized Genome-wide association study of four cashmere traits in Inner Mongolia cashmere goats was carried out using new genomics tools to infer genomic regions and functional loci associated with cashmere traits and to construct haplotypes that significantly affect cashmere traits.ResultsWe estimated the genetic parameters of cashmere traits in Inner Mongolia cashmere goats. The heritability of cashmere yield, cashmere diameter, and fleece length traits of Inner Mongolia cashmere goats were 0.229, 0.359, and 0.250, which belonged to the medium heritability traits (0.2 ~ 0.4). The cashmere thickness trait has a low heritability of 0.053. We detected 151 genome-wide significantly associated SNPs with four cashmere traits on different chromosomes, which were very close to the chromosomes of 392 genes (located within the gene or within ± 500 kb). Notch3, BMPR1B, and CCNA2 have direct functional associations with fibroblasts and follicle stem cells, which play important roles in hair follicle growth and development. Based on GO functional annotation and KEGG enrichment analysis, potential candidate genes were associated with pathways of hair follicle genesis and development (Notch, P13K-Akt, TGF-beta, Cell cycle, Wnt, MAPK). We calculated the effective allele number of the Inner Mongolia cashmere goat population to be 1.109–1.998, the dominant genotypes of most SNPs were wild-type, the polymorphic information content of 57 SNPs were low polymorphism (0 < PIC < 0.25), and the polymorphic information content of 79 SNPs were moderate polymorphism (0.25 < PIC < 0.50). We analyzed the association of SNPs with phenotypes and found that the homozygous mutant type of SNP1 and SNP3 was associated with the highest cashmere yield, the heterozygous mutant type of SNP30 was associated with the lowest cashmere thickness, the wild type of SNP76, SNP77, SNP78, SNP80, and SNP81 was associated with the highest cashmere thickness, and the wild type type of SNP137 was associated with the highest fleece length. 21 haplotype blocks and 68 haplotype combinations were constructed. Haplotypes A2A2, B2B2, C2C2, and D4D4 were associated with increased cashmere yield, haplotypes E2E2, F1F1, G5G5, and G1G5 were associated with decreased cashmere fineness, haplotypes H2H2 was associated with increased cashmere thickness, haplotypes I1I1, I1I2, J1J4, L5L3, N3N2, N3N3, O2O1, P2P2, and Q3Q3 were associated with increased cashmere length. We verified the polymorphism of 8 SNPs by KASP, and found that chr7_g.102631194A > G, chr10_g.82715068 T > C, chr1_g.124483769C > T, chr24_g.12811352C > T, chr6_g.114111249A > G, and chr6_g.115606026 T > C were significantly genotyped in verified populations (P < 0.05).ConclusionsIn conclusion, the genetic effect of single SNP on phenotypes is small, and SNPs are more inclined to be inherited as a whole. By constructing haplotypes from SNPs that are significantly associated with cashmere traits, it will help to reveal the complex and potential causal variations in cashmere traits of Inner Mongolia cashmere goats. This will be a valuable resource for genomics and breeding of the cashmere goat.

Polymorphism analysis of tri- and tetranucleotide repeat microsatellite markers in Hanwoo cattle.

The Hanwoo traceability system currently utilizes 11 dinucleotide repeat microsatellite (MS) markers. However, dinucleotide repeat markers are known to have a high incidence of polymerase chain reaction (PCR) artifacts, such as stutter bands, which can complicate the accurate reading of alleles. In this study, we examined the polymorphisms of the 11 dinucleotide repeat MS markers currently employed in traceability systems. Additionally, we explored four trinucleotide repeat MS markers and one tetranucleotide repeat MS marker in a sample of 1,106 Hanwoo cattle. We also assessed the potential utility of the tri- and tetranucleotide repeat MS markers. The polymorphic information content (PIC) of the five tri- and tetranucleotide repeat markers ranged from 0.663 to 0.767 (mean: 0.722), sufficiently polymorphic and slightly higher than the mean (0.716) of the current 11 dinucleotide repeat markers. Using all 16 markers, the mean PIC was 0.718. The estimated probability of identity (PI) was 3.13 × 10-12 using the 11 dinucleotide repeat markers, 7.03 × 10-6 using the five tri- and tetranucleotide repeat markers, and 2.39 × 10-17 using all 16 markers; the respective PIhalf-sibs values were 2.69 × 10-9, 1.29 × 10-4, and 3.42 × 10-13; and the respective PIsibs values were 3.89 × 10-5, 9.6 × 10-3, and 3.69 × 10-7. The probability of exclusion1 (PE1) was 0.999864 for the 11 dinucleotide repeat markers, 0.981141 for five of the tri- and tetranucleotide repeat markers, and > 0.99 for all 16 markers; the respective PE2 values were 0.994632, 0.901369, and > 0.99; and the respective PE3 values were 0.998702, > 0.99, and > 0.99. The five investigated tri- and tetranucleotide repeat MS markers can be used in combination with the 11 existing MS markers to improve the accuracy of individual identification and paternity testing in Hanwoo.

Simple sequence repeat genotyping of Colletotrichum species associated with soybean anthracnose in Uttarakhand and other states of India

AbstractAnthracnose is one of the most devastating diseases affecting soybean (Glycine max L. Merril) in India and is incited by the Colletotrichum truncatum species complex. In this study, 33 isolates of Colletotrichum spp. isolates were collected from major soybean‐growing states of India. The cultural, morphological and molecular characteristics (Internal Transcribed Spacer rDNA region) of all isolates were demonstrated. Twelve simple sequence repeat (SSR) markers were selected to amplify the genomic DNA of all isolates, to assess the genetic diversity. On the basis of morpho‐cultural and molecular characterization of three different Colletotrichum species, C. truncatum, C. cliviicola and C. cholorophyti were identified. Representative Colletotrichum isolates (Ct‐Pant, Ct‐Gur and Ct‐Gag) from each species group were found pathogenic to susceptible soybean variety (PS 1092) and fulfilled Koch's postulates. The SSR genotyping of 33 isolates revealed that all examined SSR markers exhibited a high degree of polymorphism, as indicated by the mean values of 0.51 for polymorphic information content, 1.97 for marker index and 1.99 for resolving power. For each primer, the average number of alleles per locus was 3.58. The results of Jaccard similarity coefficient‐based UPGMA (Un‐weighted Pair‐Group Method with Arithmetic Mean) cluster analysis and principal component analysis showed that isolates of the same species were clustered together, but no clear‐cut grouping was obtained on the basis of geographical distribution. Thus, it can be inferred from the study that C. truncatum accessions obtained from various geographical locations of India exhibit substantial genetic variation and a significant level of relatedness.

Molecular genetic diversity and linkage disequilibrium structure of the Egyptian faba bean using Single Primer Enrichment Technology (SPET)

Faba bean is an important legume crop. The genetic diversity among faba bean genotypes is very important for the genetic improvement of target traits. A set of 128 fab bean genotypes that are originally from Egypt were used in this study to investigate the genetic diversity and population structure. The 128 genotypes were genotyped using the Single Primer Enrichment Technology (SPET) by which a set of 6759 SNP markers were generated after filtration. The SNP markers were distributed on all chromosomes with a range extending from 822 (Chr. 6) to 1872 (Chr.1). The SNP markers had wide ranges of polymorphic information content (PIC), gene diversity (GD), and minor allele frequency. The analysis of population structure divided the Egyptian faba bean population into five subpopulations. Considerable genetic distance was found among all genotypes, ranging from 0.1 to 0.4. The highly divergent genotype was highlighted in this study and the genetic distance among genotypes ranged from 0.1 and 0.6. Moreover, the structure of linkage disequilibrium was studied, and the analysis revealed a low level of LD in the Egyptian faba bean population. A slow LD decay at the genomic and chromosomal levels was observed. Interestingly, the distribution of haplotype blocks was presented in each chromosome and the number of haplotype block ranged from 65 (Chr. 4) to 156 (Chr. 1). Migration and genetic drift are the main reasons for the low LD in the Egyptian faba bean population. The results of this study shed light on the possibility of the genetic improvement of faba bean crop in Egypt and conducting genetic association analyses to identify candidate genes associated with target traits (e.g. protein content, grain yield, etc.) in this panel.

Genetic Diversity and Construction of Core Collection of Sterculia Germplasm

Amplification of 107 Sterculia accessions with 12 ISSR primers resulted in 235 bands, the percentage of polymorphic sites was 100%, with the average number of effective alleles (Ne) of 1.2464, the average Nei’s gene diversity index (H) of 0.1556, the average Shannon's information index (I) of 0.2563, and the average polymorphism information content (PIC) of 0.8594, indicating that the collected 107 accessions had high genetic diversity. The genetic diversity was unevenly distributed among Sterculia samples collected from different provinces, and the highest value was observed in samples from Guangdong Province, followed by those from Yunnan Province, and the lowest was from Guangxi Province. The core collection construction of the 107 Sterculia accessions was carried out by using the SCR and LDSS methods, respectively, and the results showed that the LDSS method was more suitable for Sterculia germplasm. Different core collections were constructed based on sampling proportions of 35, 30, 25, 20 and 15%, respectively, the t-test and principal coordinates analysis results showed that the genetic diversity of the original germplasm can be fully represented at a sampling proportion of 30%. Bangladesh J. Bot. 53(2): 319-325, 2024 (June)

Genetic diversity of a Phascolosoma esculenta population following stock enhancement in Yueqing Bay, East China Sea

Responsible stock enhancement should aim to restore a population while ensuring uninterrupted genetic characteristics of the species. In this study, five pairs of screened microsatellite primers were used to analyze genetic diversity in a wild population (YS, before release), released population (FL), and recaptured population (HB, after release) of Phascolosoma esculenta to assess the impact of stock enhancement in Yueqing Bay. Microsatellite analysis revealed that the average numbers of alleles (Na) for the YS, FL, and HB of P. esculenta were 4.40, 5.40, and 5.40, respectively. The average effective numbers of alleles (Ne) were 2.11, 2.07, and 2.24, respectively. The average observed heterozygosity (Ho) was 0.312, 0.340, and 0.305, respectively, while the average expected heterozygosity (He) was 0.489, 0.465, and 0.496, respectively. The average polymorphic information content (PIC) was 0.425, 0.409, and 0.434, respectively. Analysis of Molecular Variance (AMOVA) revealed that most of the genetic variation was within populations. The genetic differentiation index (FST) values between the three populations were all less than 0.05. The three populations of P. esculenta all had moderate genetic diversity and there was minimal genetic differentiation between the populations, suggesting that the released P. esculenta were suitable for stock enhancement and that the current stock enhancement practices in Yueqing Bay have had no negative impact on the genetic diversity of P. esculenta.

Microsatellite analysis of genetic diversity and population differentiation of Acanthopagrus schlegelii in China

The study utilized 9 self-selected polymorphic microsatellite loci to amplify and investigate the genetic diversity and differentiation of Acanthopagrus schlegelii populations in 10 wild populations along the Chinese coast. The values of Polymorphic Information Content (PIC) ranged from 0.4433 to 0.5804, with an average value of 0.5143. The average number of alleles per locus (A) ranged from 3.0000 to 3.4444, with a mean value of 3.2333 and an overall value of 3.6667. The average number of effective alleles per locus (Ae) ranged from 2.0130 to 2.6014, with a mean value of 2.2994 and an overall value of 2.8013. The observed heterozygosity (Ho) ranged from 0.4607 to 0.5789, with an average value of 0.5278 and an overall value of 0.5261. The expected heterozygosity (He) ranged from 0.4657 to 0.5967, with an average value of 0.5183 and an overall value of 0.6224. The results of genetic differentiation showed the genetic differentiation coefficient (Fst) was 0.1806, and the gene flow (Nm) was 1.1342. The UPGMA cluster analysis indicated significant genetic differentiation among A. schlegelii populations along the Chinese coast, with the populations being divided into two groups, namely the northern and southern populations. The genetic differentiation structure of the southern population was inconsistent with its geographical distribution. This study utilized microsatellite molecular markers to investigate the genetic diversity and genetic differentiation of 10 wild A. schlegelii populations along the coast of China. The research results indicate that the genetic diversity of the 10 wild A. schlegelii populations is at a moderate level, with evidence of north-south differentiation. This provides a scientific basis for the conservation, germplasm improvement, and aquaculture of A. schlegelii resources in China. It also offers background information for recent stock enhancement and release projects and their impact on the genetic resources of A. schlegelii.

Genetic Diversity and Population Structure of a Large USDA Sesame Collection.

Sesame, Sesamum indicum L., is one of the oldest domesticated crops used for its oil and protein in many parts of the world. To build genomic resources for sesame that could be used to improve sesame productivity and responses to stresses, a USDA sesame germplasm collection of 501 accessions originating from 36 countries was used in this study. The panel was genotyped using genotyping-by-sequencing (GBS) technology to explore its genetic diversity and population structure and the relatedness among its accessions. A total of 24,735 high-quality single-nucleotide polymorphism (SNP) markers were identified over the 13 chromosomes. The marker density was 1900 SNP per chromosome, with an average polymorphism information content (PIC) value of 0.267. The marker polymorphisms and heterozygosity estimators indicated the usefulness of the identified SNPs to be used in future genetic studies and breeding activities. The population structure, principal components analysis (PCA), and unrooted neighbor-joining phylogenetic tree analyses classified two distinct subpopulations, indicating a wide genetic diversity within the USDA sesame collection. Analysis of molecular variance (AMOVA) revealed that 29.5% of the variation in this population was due to subpopulations, while 57.5% of the variation was due to variation among the accessions within the subpopulations. These results showed the degree of differentiation between the two subpopulations as well as within each subpopulation. The high fixation index (FST) between the distinguished subpopulations indicates a wide genetic diversity and high genetic differentiation among and within the identified subpopulations. The linkage disequilibrium (LD) pattern averaged 161 Kbp for the whole sesame genome, while the LD decay ranged from 168 Kbp at chromosome LG09 to 123 Kbp in chromosome LG05. These findings could explain the complications of linkage drag among the traits during selections. The selected accessions and genotyped SNPs provide tools to enhance genetic gain in sesame breeding programs through molecular approaches.

Genetic diversity, chemical constituents and anatomical analysis of eight popular Olive (Olea europaea L.) cultivars in Al-Jouf region, Saudi Arabia

In light of the multitude of olive trees cultivated and the lack of the genetic diversity of available genotypes to select varieties and lines that are characterized by high diversity and better performance under the corresponding conditions, A comparison analysis of the genotyping and morphological characteristics of eight olive cultivars growing in Saudi Arabia’s Al-Jouf region was conducted and analyzed. Morpho-anatomical and chemical characteristics along with both inter-simple-sequence repeats (ISSRs) and start-codon-targeted (SCoT) markers were used to evaluate the genetic diversity among eight olive varieties in Al-Jouf, Saudi Arabia. Analyses of 27 morphological, chemical, and anatomical characteristics concluded the existence of genetic differences among the studied varieties. Moreover, six ISSR and eight SCoT primer combinations produced a total of 48 loci, of which 18 (10 ISSR and 8 SCoT) were polymorphic. The average polymorphism information content (PIC values of 0.48 and 0.44, respectively) and marker index (MI of 0.79 and 0.48, respectively) detected for ISSR and SCoT markers revealed the prevalence of high genetic diversity among the studied olive varieties. Based on chemical and anatomical characteristics and the selected molecular markers, the eight olive cultivars were grouped into two distinct clusters. Clusters in the adjacent joint dendrogram produced using ISSR, SCoT and combined data were similar, and grouped all individuals into two groups. However, the dendrogram generated on the basis of SCoT separated individuals into subgroups containing at least two varieties. The findings showed that both methods were effective in assessing diversity, and that SCoT markers can be used as a reliable and informative method for assessing genetic diversity and relationships among olive varieties and can serve as a complementary tool to provide a more complete understanding of the genetic diversity available in Olea europaea populations in Saudi Arabia.

Genome-wide development of simple sequence repeats markers and genetic diversity analysis of chayote

BackgroundChayote is a high economic crop in the Cucurbitaceae family, playing an important role in food production, disease treatment and the production of degradable materials in industries. Due to the harsh environment, such as high temperature, drought and frost, some chayote resources are gradually disappearing. It is crucial to collect, characterize, and conserve chayote resources. However, the genetic diversity of chayote resources in China has not been studied so far.ResultsIn this study, we collected 35 individuals of chayote from 14 provinces in China. Subsequently, we found 363,156 SSR motifs from the chayote genome and designed 57 pairs of SSR primers for validation. Out of these, 48 primer pairs successfully amplified bands, with 42 of them showing polymorphism. These 42 primer pairs detected a total of 153 alleles, averaging 3.64 alleles per locus. The polymorphic information content ranged from 0.03 to 0.78, with an average value of 0.41, indicating a high level of polymorphism. Based on the analysis using STRUCTURE, PCoA, and UPGMA methods, the 35 chayote individuals were divided into two major clusters. Through further association analysis, 7 significantly associated SSR markers were identified, including four related to peel color and three related to spine.ConclusionsThese molecular markers will contribute to the analysis of genetic diversity and genetic breeding improvement of chayote in the future.

Polymorphism of growth hormone (GH/HaeIII) gene and its association with the performance of merino cross rams

Merino cross sheep (75% Merino × 25% Garut) are introduced by the government of Indonesia for meat production purposes. The present study aimed to determine the polymorphism in the exon 2 region of the growth hormone (GH) gene (422 bp) in Merino cross rams using the PCR-RFLP technique and to analyze its relationship with body weight and body measurements of the rams. A total of 145 rams aged one-year-old with an average body weight of 29.08 ± 7.96 kg from the breeding station in West Java, Indonesia were considered as the experimental animals. It was indicated that a missense mutation of c.55G &gt; A (p.G19S) was detected in the target sequence of the GH gene in Merino cross rams. The PCR-RFLP analysis in the GH gene of Merino cross with HaeIII restriction enzyme (GH/HaeIII) was observed in a moderate category with a polymorphic informative content (PIC) value of 0.22. Therefore, the G allele was more frequent than the A allele (0.85 versus 0.15). Furthermore, the genotype AA was not present among the sheep that were part of the study. However, the polymorphism of p.G19S was found to have no significant association with birth weight and body measurements in one-year-old Merino cross sheep. However, the GH/HaeIII gene in Merino cross rams exhibited polymorphism, primarily with two genotypes: GG (wildtype) and GA (carrier). The G allele was identified as the dominant allele in the ovine GH gene, occurring with a frequency of 0.85. Importantly, the polymorphism of the GH/HaeIII gene was significantly linked to birth weight and chest depth in one-year-old Merino cross rams. These findings provide preliminary insights that could potentially aid in the early stages of molecular selection for Indonesian Merino cross sheep.

The development of novel genome-SSRs, multiplex PCR panels, and allelic ladders for parentage identification in Tachypleus tridentatus

Tachypleus tridentatus, one of the oldest animal species on Earth, with significant biological and ecological value, its population sizes have declined due to overfishing. Stock enhancement technology has been used to protect T. tridentatus, however, its efficiency needs to be addressed. In the present study, a parentage identification system was developed. We identified 235,336 SSRs and 182,394 primer pairs were designed. Out of 321 synthesized primers, 14 highly polymorphic primers were selected to reveal the genetic diversity of 110 T. tridentatus. SSRs were amplified with the 14 developed primers, which were fluorescently labeled, and the resulting PCR products were analyzed using the ABI DNA Analyzer 3730xl. The number of alleles per locus, the polymorphism information content, the observed heterozygosity, and the expected heterozygosity ranged from 7 to 48, 0.581 to 0.963, 0.636 to 0.909, and 0.645 to 0.969, respectively. The cumulative exclusion probability with both unknown parents, with only unknown parents, or with both known parents was >99.9999% for the 14 loci. Furthermore, to facilitate data exchange across laboratories and platforms, multiplex PCR detection, SSR fragment size ladders, and parentage identification were employed. Out of the 14 primers, 6 optimal primers were selected for multiplex PCR validation, and two sets of triplex systems were established. Three thousand clones for 160 alleles of the six primers were selected for plasmid extraction and sequencing, and 600 correct plasmids were obtained for new T. tridentatus SSR fragment size ladder construction. Two pairs of parents with 12 offspring each were used for parentage identification by the multiplex PCR systems and ladders, the cumulative average exclusion probability of these 6 primers reached 99.9999% among parents and their offsprings, and was 0% in nonparent-offspring group. The parentage identification system constructed in this study can serve as a tool for monitoring the survival rates of T. tridentatus in stock enhancement programs.

Analysis of genetic diversity by the SLAF-seq among the farmed Onychostoma macrolepis populations

ObjectiveThe objective of this study was to examine the genetic diversity within and between farmed populations of Onychostoma macrolepis, and to establish a foundation for enhancing the genetic resources of breeding groups through the introduction of new individuals and crossbreeding. A total of 49 individuals were subjected to sequencing using Specific-Locus Amplified Fragment Sequencing (SLAF-seq), one of the restriction site-associated DNA sequencing technologies. The single nucleotide polymorphisms(SNPs)were identified to conduct the analyzation of phylogeny population structure, principal component and genetic diversity.ResultsA total of 853,067 SNPs were identified. The results of the phylogenetic analysis revealed that each sample was genetically clustered into three distinct groups: ZhenPing (ZP), LanGao parents (LG), and their progeny population (LG-F1). Each population was observed to be clustered together. Analysis of population genetic diversity revealed that the observed heterozygosity (Ho) ranged from 0.200 to 0.230, the expected heterozygosity (He) ranged from 0.280 to 0.282, and the polymorphic information content (PIC) ranged from 0.228 to 0.230. These results indicate that the genetic diversity of the population is low and the signs of long-term interbreeding are obvious, but there are differences between the populations, and the genetic diversity of the population can be improved by hybridization in different regions.