Number Of Alleles Research Articles

Divergence and serial colonization shape genetic variation and define conservation units in Asian elephants

Asian elephants (Elephas maximus) are the largest extant terrestrial megaherbivores native to Asia, with 60% of their wild population found in India. Despite ecological and cultural importance, their population genetic structure and diversity, demographic history, and ensuing implications for management/conservation remain understudied. We analyzed 34 whole genomes (between 11× and 32×) from most known elephant landscapes in India and identified five management/conservation units corresponding to elephants in Northern (Northwestern/Northeastern), Central, and three in Southern India. Our data reveal signatures of divergence and serial colonization and a potential dilution of genetic diversity from north to south of India. The northern populations diverged from others more than 70,000 years ago, have higher genetic diversity, and have low inbreeding (pi= 0.0016± 0.0001; FROH>1 MB= 0.09± 0.03). Two of three populations in Southern India have low diversity and are inbred, with very low effective population sizes compared with census sizes (pi= 0.0014± 0.00009 and 0.0015± 0.0001; FROH>1 MB= 0.25± 0.09 and 0.17± 0.02). Analyses of genetic load reveal the purging of potentially high-effect insertion/deletion (indel) deleterious alleles in the southern populations and a decreasing number of deleterious alleles from north to south in India. However, despite dilution and purging for the damaging mutation load in Southern India, the load that remains is homozygous. High homozygosity of deleterious alleles, coupled with low neutral genetic diversity, make southernmost populations high priority for conservation attention. Most surprisingly, our study suggests that patterns of genetic diversity and genetic load can correspond to genomic signatures of serial founding events, even in large, highly mobile, endangered mammals.

Systematic Modeling of Risk-Associated Copy Number Alterations in Cancer.

The determination of the cancer prognosis is paramount for patients and medical personnel so that they can devise treatment strategies. Transcriptional-based signatures and subtypes derived from cancer biopsy material have been used in clinical practice for several cancer types to aid in setting the patient prognosis and forming treatment strategies. Other genomic features in cancer biopsies, such as copy number alterations (CNAs), have been underused in clinical practice, and yet they represent a complementary source of molecular information that can add detail to the prognosis, which is supported by recent work in breast, ovarian, and lung cancers. Here, through a systematic strategy, we explored the prognostic power of CNAs in 37 cancer types. In this analysis, we defined two modes of informative features, deep and soft, depending on the number of alleles gained or lost. These informative modes were grouped by amplifications or deletions to form four single-data prognostic models. Finally, the single-data models were summed or combined to generate four additional multidata prognostic models. First, we show that the modes of features are cancer-type dependent, where deep alterations generate better models. Nevertheless, some cancers require soft alterations to generate a feasible model due to the lack of significant deep alterations. Then, we show that the models generated by summing coefficients from amplifications and deletions appear to be more practical for many but not all cancer types. We show that the CNA-derived risk group is independent of other clinical factors. Furthermore, overall, we show that CNA-derived models can define clinically relevant risk groups in 33 of the 37 (90%) cancer types analyzed. Our study highlights the use of CNAs as biomarkers that are potentially clinically relevant to survival in cancer patients.

Screening a new set of microhaplotypes in exonic regions for sample identity testing and paternity testing during whole exome sequencing analysis.

Whole exome sequencing (WES) is widely used in clinical diagnosis. Before obtaining an accurate diagnosis, it is essential to conduct sample identity testing and paternity testing on trio samples. Currently, there is a lack of optimal genetic markers for these purposes, with limited literature available in this area. Microhaplotypes (MHs) are promising genetic markers due to their high polymorphism, low mutation rate, short amplified fragments, absence of stutter and amplification bias. These characteristics make them suitable for sample tracking and paternity testing during WES analysis. In this study, we screened out a set of polymorphic MHs in exonic regions for the above purposes. The results showed that the power of discrimination (PD) and probability of exclusion (PE) of this set of markers ranged from 0.2682 to 0.8878 and 0.0178 to 0.4583, respectively. Both the cumulative power of discrimination (CPD) and cumulative probability of exclusion (CPE) exceeded 0.999999, indicating the great value of these markers in paternity testing and individual identification in the study population. However, these markers had the effective number of alleles (Ae) values ranging from 1.1784 to 3.8727 (average 2.1805) and informativeness (In) values ranging from 0.0151 to 0.2209 (average 0.0766), showing limited value in DNA mixture analysis and biogeographical ancestry inference.

Genetic Diversity and Selection Signal Analysis of Hu Sheep Based on SNP50K BeadChip.

This research is designed to examine the genetic diversity and kinship among Hu sheep, as well as to discover genes associated with crucial economic traits. A selection of 50 unrelated adult male Hu sheep underwent genotyping with the SNP50K BeadChip. Seven indicators of genetic diversity were assessed based on high-quality SNP data: effective population size (Ne), polymorphic information content (PIC), polymorphic marker ratio (PN), expected heterozygosity (He), observed heterozygosity (Ho), effective number of alleles, and minor allele frequency (MAF). Plink software was employed to compute the IBS genetic distance matrix and detect runs of homozygosity (ROHs), while the G matrix and principal component analysis were performed using GCTA software. Selective sweep analysis was carried out using ROH, Pi, and Tajima's D methodologies. This study identified a total of 64,734 SNPs, of which 56,522 SNPs remained for downstream analysis after quality control. The population displayed relatively high genetic diversity. The 50 Hu sheep were ultimately grouped into 12 distinct families, with families 6, 8, and 10 having the highest numbers of individuals, each consisting of 6 sheep. Furthermore, a total of 294 ROHs were detected, with the majority having lengths between 1 and 5 Mb, and the inbreeding coefficient FROH was 0.01. In addition, 41, 440, and 994 candidate genes were identified by ROH, Pi, and Tajima's D methods, respectively, with 3 genes overlapping (BMPR1B, KCNIP4, and FAM13A). These results offer valuable insights for future Hu sheep breeding, genetic assessment, and population management.

Development of microsatellite markers and evaluation of the genetic diversity of the edible sea anemone Paracondylactissinensis (Cnidaria, Anthozoa) in China.

Paracondylactissinensis Carlgren, 1934 is a sea anemone with economic value in China. The wild population of P.sinensis has been shrinking due to overfishing and environmental pollution, which have caused price instability. In winter, the price of P.sinensis can reach 25 USD per kilogram. Up to now, there are no genetic markers developed for P.sinensis, preventing a further exploration of their population genetic diversity. In this study, the full-length transcriptome of P.sinensis was sequenced and microsatellite DNA markers (simple sequence repeats [SSRs]) were developed from those transcripts. A total of 52 primer pairs, which can amplify specific polymorphic bands in PCR experiments, were designed for the SSR markers. Genetic diversity and population genetics were analysed for P.sinensis populations collected from the coasts of Taizhou and Rizhao using six microsatellite DNA loci. While inbreeding was detected in both populations (Fis > 0), the overall number of alleles (Na = 11.3) and bottleneck analysis suggested that the genetic diversity of P.sinensis has not been greatly impacted. Clustering analyses using STRUCTURE, principal coordinate analysis and unweighted pair group method with arithmetic mean tree revealed that the Taizhou population diverged from the Rizhao population; however, the genetic differentiation between the populations was moderate. Human-mediated commercial activities may be the principal reasons for the gene flow between the populations. Our study provides the first evaluation of the genetic resources of wild P.sinensis populations in China, which can serve as a useful reference for future comparative studies on population genetics and may guide policy-makers in initiating strategies for germplasm conservation and artificial breeding.

Exploring Sampling Strategies and Genetic Diversity Analysis of Red Beet Germplasm Resources Using SSR Markers

By using 14 SSR primer pairs, we here analyzed and compared the amplification results of 534 DNA samples from six red sugar beet germplasm resources under three treatments. These data were used to explore the sampling strategy for the aforementioned resources. Based on the sampling strategy results, 21 SSR primer pairs were used to evaluate the genetic diversity of 47 red sugar beet germplasm resources. The six population genetic parameters used for exploring the sampling strategy unveiled that individual plants within the population had a relatively large genetic distance. The genetic parameters Ne, I, and Nei’s of the randomly mixed sampling samples increased rapidly between 10 and 30 plants before decreasing. Therefore, when SSR technology was used to analyze the genetic diversity of the red sugar beet germplasm resources, the optimal sampling gradient for each population was the adoption of a random single-plant mixed sampling sample of no less than 10 plants and no more than 30 plants. The 21 SSR primer pairs were used to detect genetic diversity in 30 random mixed samples of 47 resources. The average polymorphic information content (PIC) was 0.5738, the average number of observed alleles (Na) was 4.1905, the average number of effective alleles (Ne) was 2.8962, the average Shannon’s information index (I) was 1.1299, the average expected heterozygosity (Nei’s) was 0.6127, and the average expected heterozygosity (He) was 0.6127. The genetic distance of the 47 germplasm resources ranged from 0.0225 to 0.551 (average: 0.316). According to the population structure analysis, the most suitable K value was six, which indicated the presence of six populations. Based on the clustering analysis results, the 47 germplasm resources were segregated into six groups, with obvious clustering and some germplasm resources noted for having groups with close genetic relationships. We here established a more accurate and scientific sampling strategy for analyzing the genetic diversity of red sugar beet germplasm resources by using SSR molecular markers. The findings provide a reference for collecting and preserving red sugar beet germplasms and protecting their genetic diversity.

Genetic Diversity of Tulipa alberti and T. greigii Populations from Kazakhstan Based on Application of Expressed Sequence Tag Simple Sequence Repeat Markers.

The genus Tulipa L., renowned for its ornamental and ecological significance, encompasses a diversity of species primarily concentrated in the Tian Shan and Pamir-Alay Mountain ranges. With its varied landscapes, Kazakhstan harbors 42 Tulipa species, including the endangered Tulipa alberti Regel and Tulipa greigii Regel, which are critical for biodiversity yet face significant threats from human activities. This study aimed to assess these two species' genetic diversity and population structure using 15 expressed sequence tag simple sequence repeat (EST-SSR) markers. Leaf samples from 423 individuals across 23 natural populations, including 11 populations of T. alberti and 12 populations of T. greigii, were collected and genetically characterized using EST-SSR markers. The results revealed relatively high levels of genetic variation in T. greigii compared to T. alberti. The average number of alleles per locus was 1.9 for T. alberti and 2.8 for T. greigii. AMOVA indicated substantial genetic variation within populations (75% for T. alberti and 77% for T. greigii). The Bayesian analysis of the population structure of the two species indicated an optimal value of K = 3 for both species, splitting all sampled populations into three distinct genetic clusters. Populations with the highest level of genetic diversity were identified in both species. The results underscore the importance of conserving the genetic diversity of Tulipa populations, which can help develop strategies for their preservation in stressed ecological conditions.

Molecular fingerprinting of highly resistant maize lines to turcicum leaf blight

AbstractThe present study generates information related to the molecular divergence between turcicum leaf blight (TLB)-resistant and -susceptible lines. During molecular diversity studies, a total of 212 alleles were detected at 75 marker loci and ranged from two to five with an average of 2.83 alleles per locus. A direct correlation for the number of alleles and polymorphism information content (PIC) values was ascertained. For instance, marker phi123 produced high number of alleles (5) with PIC values of 0.77. Using the DARwin 6.0 programme, the UPGMA dendrogram grouped 40 maize inbreds into two distinct clusters, cluster-I (36 inbreds) and cluster-II (4 inbreds). Cluster-I contained two subclusters; the first subcluster contained 28 inbreds and the second subcluster contained eight inbreds whereas cluster-II contained four inbreds. This major cluster-II was further classified into two subclusters which contained two inbreds each. Most of the inbred lines except V-25 from cluster-II were highly resistant to TLB disease. These inbred lines can be used in crossing programmes to develop TLB-resistant hybrids by using divergent parents. In this study, allelic diversity and PIC values indicated a good efficiency of markers for studying the polymorphism level available in studied inbred lines. High level of diversity among the inbreds detected with simple sequence repeat markers indicated their suitability for the further breeding programme.

Genetic Diversity and Population Genetic Structure of Jatropha curcas L. Accessions from Different Provenances Revealed by Amplified Fragment-Length Polymorphism and Inter-Simple Sequence Repeat Markers

The genetic diversity and structure of 17 populations of J. curcas, including 92 accessions from different provenances (tropical and subtropical), were investigated and effectively evaluated using twelve inter-simple sequence repeats (ISSRs) and seven pairs of florescence-amplified fragment-length polymorphism (AFLP) primers. Genetic diversity, at the overall level among populations of J. curcas based on the ISSR markers, showed that the observed number of alleles (Na) was 1.593, the effective number of alleles (Ne) was 1.330, Nei’s gene diversity (H) was 0.200, Shannon’s information index (I) was 0.303, and the percentage of polymorphic loci was 59.29%, indicating moderate genetic diversity between and within the different populations of J. curcas. Based on the genetic diversity analysis of AFLP markers, there were 1.464 (Na) and 1.216 (Ne) alleles, Nei’s gene diversity (H) was 0.132, Shannon’s information index (I) was 0.204, and the percentage of polymorphic loci was 46.40%. The AMOVA analysis showed that this large variance was due to differences within the populations, with genetic distinctions and limited gene flow among those from varied regions. The 17 populations were clustered into five main groups via UPGMA clustering analysis based on Nei’s genetic distance, and the genetic relationships among the populations exhibited no significant correlations with geographical provenances. The genetic variation among Chinese populations of J. curcas distributed in dry-hot valley areas was remarkable, and the American germplasm presented with distinct genetic differentiation.

CFTR complex alleles and phenotypic variability in cystic fibrosis disease.

Cystic fibrosis (CF) is inherited by CFTR (cystic fibrosis transmembrane conductance regulator) gene mutations. A variety of mutations have been identified in the CFTR gene that may be associated with cystic fibrosis, and these mutations demonstrate extensive molecular genetic heterogeneity in this disease. Little is known about the molecular mechanism by which mutations affect CFTR function, and only a minority of mutations have been characterized by functional studies. There has been an increase in the number of complex alleles. This may partly explain the difficulty in establishing genotype-phenotype correlations and complicate genetic counseling and diagnosis in some cases. Therefore, the identification of complex alleles has several important implications for recessive disorders. This will facilitate diagnosis; improve judgements concerning prognosis, and enable appropriate genetic counselling for affected families. This review describes the complex cystic fibrosis allele to better understand the contribution of this allele in the wide phenotypic variability of cystic fibrosis disease. It occurs in the complex allele that the second cis mutation can modulate the effects of the first mutation or vice versa. The phenotypic variability between CF or CFTR-RD (CFTR related disease) patients may be due to several factors, including different genetic and environmental backgrounds. It is important to determine the allele complex so that optimal treatment can be established.

GENETIC DIVERSITY AND POPULATION STRUCTURE OF JUNIPERUS SERAVSCHANICA KOM. IN CENTRAL ASIA REVEALED BY MICROSATELLITE MARKERS

Juniperus seravschanica Kom. is a widely distributed and significant tree species in Central Asia, thriving in the mountain ranges from Oman to Uzbekistan, Kyrgyzstan, and Kazakhstan. It plays a vital role in forming shrub-forest massifs in mountainous regions, contributing to soil drainage and stabilization at medium to high altitudes. To gain a detailed understanding of the current status of J. seravschanica and to develop effective conservation strategies, a comprehensive study of the species' genetic diversity and population structure was conducted. Leaf samples were collected from 15 J. seravschanica populations across Uzbekistan, Kyrgyzstan, and Kazakhstan to assess genetic diversity and population structure. Using 11 polymorphic simple sequence repeat (SSR) markers, genetic diversity parameters such as the number of alleles, the number of effective alleles, the percentage of polymorphic loci, and Nei's genetic diversity index were evaluated. Nei's genetic diversity index for J. seravschanica populations averaged 0.450, ranging from 0.407 to 0.566. The AMOVA revealed that 90.3% of the total genetic variation was within populations, indicating a high level of genetic diversity within each population. Gene flow, calculated using alleles from all populations, was estimated at 4.654. Population structure analysis showed weak clustering among the studied populations, supporting the AMOVA findings. This study provides valuable insights into the genetic diversity and population structure of J. seravschanica in Central Asia. The high genetic diversity within populations suggests a strong adaptive capacity to environmental changes. These findings can be effectively utilized to develop conservation strategies for J. seravschanica, ensuring the long-term sustainability of this important tree species in Central Asia. This work was supported by Grant No.AP09259027 of the Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan.

Individual Identification and Assessment of Genetic Diversity Using Microsatellite Markers in Racing Pigeons Raised in Turkiye

The implementation of a swift and economical molecular genetic approach, ensuring both efficacy and cost-effectiveness and facilitating population certification, is of utmost significance for breeders and the conservation of Turkiye's native pigeon biodiversity. In this study, we aimed to examine the genetic structure of racing pigeons (Columba livia domestica) raised in Turkiye using a genetic marker panel consisting of eight short tandem repeat (STR) loci. For this purpose, DNA was isolated from the shed feathers of 216 pigeons. Genomic DNA was amplified using the multiplex allele-specific PCR and subsequent capillary electrophoresis with ABI PRISM 3130XL Genetic Analyzer. Next, PCR products were analyzed in the GeneMapper Software program (Applied Biosystems). For parent testing, paternity index (PI), combined paternity index (CPI), and cumulative probability of paternity (CPP) were calculated. Furthermore, population genetic diversity was evaluated using heterozygosity (He), polymorphism information content (PIC), and Hardy–Weinberg equilibrium (HWE) testing. Results revealed that the total number of alleles is 81 and the number of alleles per locus varies between 4 and 19. The similarity rate between parent and offspring was calculated as 99.99% and above. Since no pedigree information was given when the samples were analyzed, obtaining this similarity ratio demonstrates the reliability of the panel. He values range from 0.362 to 0.919, and the PIC values range from 0.295 to 0.909. Loci PG-1, PG-2, and PG-3 show significant genetic diversity, with moderate to high PIC values reflecting varied allele frequencies in the population. Consequently, the set of seven STR markers (+ one sex marker) can be applied to identify and confirm parentage on a regular basis, thereby facilitating efficient breeding programs and ensuring genetic diversity conservation. This panel enables efficient pedigree analysis and gender determination, optimizing cost-effectiveness. The methodology presented in this study is ideal for pedigree analysis and breed certification in the Turkish pigeon breeding industry. Consequently, we affirm that the study data carries considerable national importance.

Multiple glacial refugia during Pleistocene climatic oscillations shape the genetic pattern of Machilus thunbergii across East Asia

Abstract Pleistocene climatic oscillations caused periodic decline and rise of sea levels, leading to dispersion and retraction cycles of island flora. Yet, the role of island refugia in the current Sino-Japanese Floristic Region remains poorly understood. In this study, we investigated the population genetic structure of the widespread Sino-Japanese Floristic Region tree Machilus thunbergii to infer the potential impact of island refugia. We collected 1378 samples from 64 locations across the distribution ranges. Using chloroplast DNA and microsatellite markers, we found a pronounced genetic differentiation between mainland and island populations, which can be divided further into two and three groups, respectively. Furthermore, comparable numbers of private alleles and haplotypes are present in both mainland and island populations. No essential current gene flow was detected between mainland and island populations after their separation 14 000 years ago. Such patterns are hypothesized to result from the influence of multiple glacial island refugia during Pleistocene climatic oscillations, with limited pollen and seed dispersal of the species. Our findings underscore that the islands and submerged land bridge can act as refugia for plants during glacial periods and have essentially shaped the genetic structure of M. thunbergii populations.

A decision-making framework to maximise the evolutionary potential of populations - Genetic and genomic insights from the common midwife toad (Alytes obstetricans) at its range limits

Anthropogenic habitat modification and climate change are fundamental drivers of biodiversity declines, reducing the evolutionary potential of species, particularly at their distributional limits. Supportive breeding or reintroductions of individuals are often made to replenish declining populations, sometimes informed by genetic analysis. However, most approaches utilised (i.e. single locus markers) do not have the resolution to account for local adaptation to environmental conditions, a crucial aspect to consider when selecting donor and recipient populations. Here, we incorporate genetic (microsatellite) and genome-wide SNP (ddRAD-seq) markers, accounting for both neutral and putative adaptive genetic diversity, to inform the conservation management of the threatened common midwife toad, Alytes obstetricans at the northern and eastern edges of its range in Europe. We find geographically structured populations (n = 4), weak genetic differentiation and fairly consistent levels of genetic diversity across localities (observed heterozygosity and allelic richness). Categorising individuals based on putatively adaptive regions of the genome showed that the majority of localities are not strongly locally adapted. However, several localities present high numbers of private alleles in tandem with local adaptation to warmer conditions and rough topography. Combining genetic diversity and local adaptations with estimates of migration rates, we develop a decision-making framework for selecting donor and recipient populations which maximises the geographic dispersal of neutral and putatively adaptive genetic diversity. Our framework is generally applicable to any species, but especially to amphibians, so armed with this information, conservationists may avoid the reintroduction of unsuitable/maladapted individuals to new sites and increase the evolutionary potential of populations within species.

Exploration of Genetic Variation and Population Structure in Bergenia ciliata for its Conservation Implications.

Bergenia ciliata (Haw.)Sternb. is a perennial medicinal herb distributed in Indian Himalayan Region(IHR). A total of eight populations of B.ciliata were collected from diverse locales of IHR, and 17 EST-SSR markers were used in this study. The present study revealed moderate genetic diversity at the locus level with the mean number of alleles (Na = 7.823), mean number effective of alleles (Ne = 3.375), mean expected heterozygosity (He = 0.570), and meanShannon's diversity index (I = 1.264). The MSR (He = 0.543, I = 1.067) and DRJ populations (He = 0.309, I = 0.519) revealed the highest and lowest genetic diversity at the population level, respectively. AMOVA analysis showed that 81.76% of genetic variation was within populations, 10.55% was among populations, and 7.69% was among the regions. In addition, a moderate to high level of differentiation was found among the populations (FST = 0.182), which could be indicative of low to moderate gene flow (Nm = 0.669) in the B. ciliata populations. UPGMA and PCoA analysis revealed that eight populations could be differentiated into two groups, while the structure analysis of the 96 individuals differentiated into three groups. The Mantel test showed a positive relationship between genetic and geographical distance. The findings of this study will provide the development of conservation and germplasm management strategies for this valuable medicinal species.

Detection of the effect of the KISS1 gene on reproductive parameters in Saanen goats

The KISS1 gene, which activates G protein-coupled receptor-54 (GPR54) and plays a crucial role in the neuroendocrine regulation of GnRH secretion, is known to encode a family of neuropeptides called kisspeptins. Therefore, the KISS1 gene is thought to be associated with sexual maturity, offspring development, and estrus. The g.2124T>A polymorphism of the KISS1 gene, is believed to affect the reproductive system, has been studied in Indonesian goat breeds, Damascus, Zarabi, Baladi, Gaddi, Kaligesing, Guanzong, Xinong Saanen and Boer goat breeds until now. These studies are generally related determining polymorphism frequencies or the effect of genotype on litter size. The study aims to determine the allele and genotype frequencies of the KISS1 gene g.2124T>A SNP by the PCR-RFLP method and define the relationship between the genotypic structures and reproductive parameters such as luteal growth, maximum corpus luteum diameter, and mating rate in Saanen goats (n=30). According to the results, the genotype frequencies in Saanen goats for the KISS1 gene g.2124T>A were 10.35%, 55.17%, and 34.48% for AA, TT and AT, respectively. Moreover, the genotypic structure did not have a statistically significant effect on the investigated fertility characteristics. The average values of expected heterozygosity (He), observed heterozygosity (Ho), the effective number of alleles (Ne), fixation index values (FIS), and the polymorphism information content (PIC) were 0.3996, 0.3448, 1.6655, 0.8629 and 0.855, respectively. The Hardy-Weinberg chi square (χ2) value was found to be 0.5435. In conclusion, it was found necessary to study the KISS1 - g.2124T>A polymorphism in larger herds with different gene pools as a reason for the existence of genotypic variation and the narrow population size.

Development and characterization of polymorphic microsatellite markers for Periplaneta americana (Blattodea: Blattidae).

The American cockroach, Periplaneta americana (Blattodea: Blattidae), is a prevalent urban pest with significant public health implications. This study aimed to develop and validate novel microsatellite markers to understand the genetic diversity and population genetic structure of P. americana. In this study, a total of 397,898 microsatellite markers were developed based on 24.6 million genomic DNA sequences. Twenty microsatellite markers were selected and amplified with varying numbers of alleles ranging from 0 to 35. Seven out of 20 markers were characterized for their polymorphism and amplification efficiency. The polymorphic information content (PIC) values of these markers were high (0.669 to 0.950) implying their effectiveness. These markers also revealed 7 to 35 alleles per locus across tested samples, highlighting their utility in assessing the extensive genetic variation within Periplaneta americana populations. These results provide insightful information that may be applied to the genetic analysis of the American cockroach population using the developed species-specific microsatellite marker.

Mating Strategy in the Arab Horse Population Over 30 Years in Algeria

Abstract The objective of this research was to describe the variation in breeding practices in the population of Arabian horses in Algeria in relation to the population size drop observed in the 2000s, due to an increase in the cost of food and a change in interest in racing, related to the black decade. As a result, the breeders had to face two opposite constraints: enhancing reproduction to counter the population decline and preventing the loss of genetic diversity. The aim of the study was to evaluate the genetic consequences of the decisions taken over a period of 30 years, starting from 1988 to 2018. The study was based on the analyses of the stud-book and on 11 microsatellite markers in a group of 943 horses, distributed into 13 age classes. Between 2004 and 2008, the breeders purchased foreign sires and dams, allowing a relative stability in unbiased heterozygosity of about 71%, due to the high genetic distances between foreign and local horses. As these importations stopped from 2009 on, there was a decrease in allele numbers of about 20%. Moreover, from 2010 on, we observe an excess of inbreeding and an increase in genetic drift relative to the starting population, due to population size decline. From the analysis of genetic distances between local individuals, it seems that the only constraint for sires and dams allowed to mate was a null coefficient of inbreeding.

Quantitative Trait Loci Mapping of Heading Date in Wheat under Phosphorus Stress Conditions.

Wheat (Triticum aestivum L.) is a crucial cereal crop, contributing around 20% of global caloric intake. However, challenges such as diminishing arable land, water shortages, and climate change threaten wheat production, making yield enhancement crucial for global food security. The heading date (HD) is a critical factor influencing wheat's growth cycle, harvest timing, climate adaptability, and yield. Understanding the genetic determinants of HD is essential for developing high-yield and stable wheat varieties. This study used a doubled haploid (DH) population from a cross between Jinmai 47 and Jinmai 84. QTL analysis of HD was performed under three phosphorus (P) treatments (low, medium, and normal) across six environments, using Wheat15K high-density SNP technology. The study identified 39 QTLs for HD, distributed across ten chromosomes, accounting for 2.39% to 29.52% of the phenotypic variance. Notably, five stable and major QTLs (Qhd.saw-3A.7, Qhd.saw-3A.8, Qhd.saw-3A.9, Qhd.saw-4A.4, and Qhd.saw-4D.3) were consistently detected across varying P conditions. The additive effects of these major QTLs showed that favorable alleles significantly delayed HD. There was a clear trend of increasing HD delay as the number of favorable alleles increased. Among them, Qhd.saw-3A.8, Qhd.saw-3A.9, and Qhd.saw-4D.3 were identified as novel QTLs with no prior reports of HD QTLs/genes in their respective intervals. Candidate gene analysis highlighted seven highly expressed genes related to Ca2+ transport, hormone signaling, glycosylation, and zinc finger proteins, likely involved in HD regulation. This research elucidates the genetic basis of wheat HD under P stress, providing critical insights for breeding high-yield, stable wheat varieties suited to low-P environments.

Polymorphism of microsatellite loci in populations of Caucasian rock lizards and its use for assessing the genetic diversity of Darevskia raddei

The study of Caucasian rock lizards of the Darevskia raddei complex, represented by several subspecies, is of great interest and scientific significance in connection with their participation in interspecific hybridizations with the formation of five of the seven known unisexual (parthenogenetic) species of the genus Darevskia. Here are presented genetic parameters for populations (subspecies) of D. r. raddei and D. r. nairensis based on the analysis of the variability of 10 microsatellite loci of 230 individuals from 17 populations of Armenia and Nagorno-Karabakh. According to these parameters, D. r. raddei are characterized by greater diversity in the number of alleles and genotypes compared to D. r. nairensis. Genetic differentiation analysis showed that D. r. raddei populations are divided into two groups, one of which is genetically closer to D. r. nairensis than D. r. raddei. Analysis of the association index showed the absence of free recombination of alleles between subspecies, which indicates their isolation and the absence of crossing between individuals. Thus, based on the expanded population sample and the developed panel of microsatellite markers, new data on the population structure of D. raddei species, genetic diversity and differentiation of D. r. raddei and D. r. nairensis were obtained.