Levels Of Heterozygosity Research Articles

Blood donor biobank and HLA imputation as a resource for HLA homozygous cells for therapeutic and research use

BackgroundAllogeneic therapeutic cells may be rejected if they express HLA alleles not found in the recipient. As finding cell donors with a full HLA match to a recipient requires vast donor pools, the use of HLA homozygous cells has been suggested as an alternative. HLA homozygous cells should be well tolerated by those who carry at least one copy of donor HLA alleles. HLA-A-B homozygotes could be valuable for HLA-matched thrombocyte products. We evaluated the feasibility of blood donor biobank and HLA imputation for the identification of potential cell donors homozygous for HLA alleles.MethodsWe imputed HLA-A, -B, -C, -DRB1, -DQA1, -DQB1 and -DPB1 alleles from genotypes of 20,737 Finnish blood donors in the Blood Service Biobank. We confirmed homozygosity by sequencing HLA alleles in 30 samples and by examining 36,161 MHC-located polymorphic DNA markers.ResultsThree hundred and seventeen individuals (1.5%), representing 41 different haplotypes, were found to be homozygous for HLA-A, -B, -C, -DRB1, -DQA1 and -DQB1 alleles. Ten most frequent haplotypes homozygous for HLA-A to -DQB1 were HLA-compatible with 49.5%, and three most frequent homozygotes to 30.4% of the Finnish population. Ten most frequent HLA-A-B homozygotes were compatible with 75.3%, and three most frequent haplotypes to 42.6% of the Finnish population. HLA homozygotes had a low level of heterozygosity in MHC-located DNA markers, in particular in HLA haplotypes enriched in Finland.ConclusionsThe present study shows that HLA imputation in a blood donor biobank of reasonable size can be used to identify HLA homozygous blood donors suitable for cell therapy, HLA-typed thrombocytes and research. The homozygotes were HLA-compatible with a large fraction of the Finnish population. Regular blood donors reported to have positive attitude to research donation appear a good option for these purposes. Differences in population frequencies of HLA haplotypes emphasize the need for population-specific collections of HLA homozygous samples.

Assessing Leaf Morphometric Symmetry of Four Chinese Quercus Species in a Mixed Forest

(1) Background: Oaks have achieved notoriety for sufficient levels of sympatric species richness allowing hybridization, thus generating substantial phenotypic variation. Leaf fluctuation asymmetry is an important attribute, as it reflects not only genetic variability but also species buffering capacity. (2) Methods: We investigated the phenotypic diversity of four-oak species (Quercus acutissima, Q. variabilis, Q. fabri, and Q. serrata var. brevipetiolata) using leaf geometric morphometric analysis. Eight leaf morphological indicators (length, width, perimeter, area, left and right areas, areal ratio, and normalized symmetry index) were used to determine the hybridization level, whereas bilateral symmetry indicators were used to assess species environmental adaptation; (3) Results: Phenotypic variation ranged from 1.54 to 29.35 folds and significantly diverged among the studied species. Taxonomically species in Section Quercus (Q. fabri and Q. serrata var. brevipetiolata) are lower than those in Section Cerris (Q. acutissima and Q. variabilis) with good bilateral symmetry. The bilateral symmetry index of Q. variabilis had a larger range of variation, indicating better environmental adaptability; (4) Conclusions: We presume that species in Section Quercus with less leaf fluctuation asymmetry have a high level of genetic heterozygosity; however, this assumption requires further verification. The observed phenotypic diversity reflects a combination of environmental and genetic factors.

Genetic diversity analysis of Eggplant Germplasm from Iran: assessments by morphological and SSR markers.

Eggplant is an important vegetable that has long been cultivated in different parts of Iran. The major objectives of the eggplant breeding program are to improve fruit quality, increase yield performance through heterosis breeding, and introduce abilities of pest and disease resistance from wild relatives. In order to select suitable parents for breeding purposes, with respect to the genetic and morphological diversity of eggplant cultivars, it is necessary to have sufficient knowledge of genetic diversity and classification of germplasms. This experiment was conducted in a randomized block design at the Seed and Plant Improvement Institute (SPII) in Karaj, Iran. Here, morphological diversity was assessed among a collection of eggplants which comprised four Iranian lines and 13 non-Iranian genotypes. For this purpose, 16 morphological traits were analyzed in the plants. Given the weakness of morphological analysis in providing precise characterizations of genetic divergence, a molecular study was also carried out by using five Simple Sequence Repeat (SSR) markers. In addition to the univariate analysis, the multi-descriptor variation was studied among the genotypes using two methods of multivariate analyses. The genotypes differed significantly in terms of the morphological traits. The multivariate analyses of morphological data indicated that eggplants from two different origins were clearly differentiated. Three main clusters were distinguished by a morphological UPGMA dendrogram in which non-Iranian genotypes, with the exception of 11,212, constituted cluster I and required the maximum number of days to flower, days to fruit set, and days to first harvest. Cluster II was identified with two Iranian lines BJ30, Y60, and one non-Iranian genotype (11,212) which showed the highest values of stem diameter, fruit diameter, fruit length, fruit length-to-width ratio, number of fruits per plant, and yield. Cluster III comprised two Iranian lines, D1 and D7, and showed the maximum plant height, number of internodes, number of nodes, number of leaves, number of stems, fruit weight, and fruits weight per plant. The highest and lowest intra-cluster genetic distances were observed in cluster I and cluster II, respectively. Based on SSR analysis, high levels of similarity were detected between several genotypes, namely, Y60 and 13,411; BJ30 and 1111; D7 and 13,521; 21,881 and 13,421. High levels of heterozygosity and polymorphism information content (PIC) were observed in this study. This not only indicated high levels of polymorphism and an equal distribution of the evaluated loci but also suggested that these genotypes can be considered for the development of diverse parental lines which are of interest in breeding programs.

Differences and changes: an evaluation of the genetic diversity of Arabian mares from Polish state studs born between 1996 and 2013

Abstract The goal of our study was to estimate genetic diversity of Arabian horses from Polish state studs which could have changed due to the extensive use of foreign sires in Polish breeding after 1989. The analysis focused on 1,388 Arabian mares born from 1996 to 2013 in the Białka, Janów Podlaski and Michałów studs. Basic parameters of pedigree, mitochondrial DNA and microsatellite analyses were considered in the study. In the pedigree analysis, changes in the gene pool over the years were noted through the considerable increase of contribution of new founders’ genes and the considerable decrease of inbreeding level. The microsatellite analysis confirmed progressive changes in the gene pool but, contrary to expectations, only three new microsatellite alleles were detected, and a decreased level of heterozygosity was observed. In turn, mtDNA analysis showed a stable genetic situation in the studs throughout the period analysed. The results of the analyses present a diverse picture of the population, which is clearly divided into the three subpopulations of Białka, Janów Podlaski and Michałów, although the pictures presented differed depending on the analytical methods used. Genetic differences among the studs should be considered a positive feature of the Polish population. In order to preserve the present level of population genetic diversity, changes in breeding policy are needed that aim to stop the loss of genes of the historical ancestors of Polish Arabian horses.

ABCL-371 STR Loci Allele Imbalance at 9p24.1 in Primary Mediastinal B-Cell Lymphoma

Molecular factors that determine the prognosis of immunotherapy response in primary mediastinal B-cell lymphoma (PMBCL) are not yet described. PD-L1/L2 expression levels in tumor samples have demonstrated clinical utility for many solid tumors. PD-L1/L2 expression levels could be affected by chromosomal lesions on 9p24.1 (losses or gains). Short tandem repeat (STR) analysis of appropriate markers is the simplest way to detect these lesions. To analyze possible associations between STR loci allele imbalance (AI) on 9p24.1 and PD-L1 expression levels in tumor cells from PMBCL patients. Two STR Loci (gt) n and (ttat)m on 9p24.1 in tumor cells were analyzed for a cohort of 36 PMBCL patients admitted to the National Medical Research Center for Hematology (Moscow, Russia) from 2013 to 2022. For six patients, STR data were compared with PD-L1 expression assessed by immunohistochemistry. DNA was isolated from tumor biopsy samples taken at diagnosis. Control DNA samples were taken from the blood of patients in complete remission or from the buccal epithelium. STR analysis for AI was performed by PCR with original primers. The fragment analysis was performed on an ABI3130 Genetic Analyzer. Inclusion criteria: de novo diagnosed PMBCL patients. pretreatment. The heterozygosity level for the (gt)n locus was 31 of 36 patients (86%), and AI was found in 16 of 31 (51.6%). The heterozygosity level for the (ttat)m locus was 20 of 36 patients (56%), and AI was found in 9 of 20 (45%). One patient was homozygous for both loci. No patients were found with AI at one locus and a normal heterozygous variant at the second locus. PD-L1 expression in tumor cells was evaluated for six patients. In two patients with aberrant STR loci, PD-L1 expression was found in 75%-100% of tumor cells. None of the four patients with normal 9p24.1 STR markers had PD-L1-positive cells. The high incidence of AI in the 9p24.1 locus indicates its possible involvement in the pathogenesis of PMBCL. The association between AI and PD-L1 expression in tumor cells requires confirmation in an extended cohort of patients. This study was supported by Rakfond grant 2/2020.

Heterozygosity reduction in children whose parents are closely related

In this study, the impact of consanguineous marriage and inbreeding on heterozygosity was evaluated by comparing levels of heterozygosity in children of closely related parents with those of unrelated parents. Compared to the average expected heterozygosity, the average observed heterozygosity was lower in the children with first-cousin parents. This was not the case in the children with unrelated parents, where an increase in the average observed heterozygosity was noted. Differences in the average heterozygosity between parents-children also observed between related and unrelated parents. First-cousin parents had higher average heterozygosity than the children compared to the unrelated parents where the average heterozygosity was lower than the children. Further investigation with bigger sample size and different populations will provide better understanding, however this study showed that a careful approach should be taken when dealing with parentage testing involving closely related parents.

Simple Sequence Repeats-Based Genetic Characterization and Varietal Identification of Potato Varieties Grown in Pakistan

The potato (Solanum tuberosum L.) is an important cash crop with a complex genome and with features of aneuploidy with a high level of heterozygosity. It is a prerequisite for potato breeding to have knowledge of genetic diversity and population structure. To understand the genetic characteristics of potato cultivars in Pakistan, 25 potato varieties were characterized with simple sequence repeat (SSR) markers to distinguish closely related varieties. In total, 214 alleles were amplified with 35 SSR markers exhibiting 89.2% polymorphism. The maximum number of alleles and polymorphic alleles per locus were 20 and 14 for the markers S25 and S174, respectively. The polymorphic information content (PIC) extended from 0.00–0.87. The size of the amplified PCR product ranged between (30–1000 bp). A cluster analysis divided the 25 varieties into three clusters: cluster I revealed the most diversity, followed by cluster II with 11 varieties and cluster III with 13 varieties. Nei’s genetic diversity and minimum spanning network (MSN) depicted the Mozika variety as the most diverse compared to the rest of the varieties. Nei’s coefficient was found to vary from 0.53 to 0.95. Out of the 25 studied varieties, 16 were uniquely identified by 29 polymorphic SSR bands of different sizes with a maximum size amplified by S4026/4027 (800bp) and a minimum by S170 (90bp). The genetic diversity and varietal identification determined in the present study has molecular and breeding-related significance with respect to the utilization and protection of intellectual property rights of potato cultivars for sustainable potato production in Pakistan.

Hemp Growth in Vitro and in Vivo: A Comparison of Growing Media and Growing Environments across 10 Accessions

Micropropagation is a valuable production tool for the cultivation of hemp (Cannabis sativa), and development of optimal protocols is ongoing. The goal of this study was to evaluate a novel growing medium combination, consisting of Driver and Kuniyuki Walnut (DKW) medium as the nutrient source and glucose as the carbon source, and to investigate the link between in vitro and in vivo (i.e., greenhouse) plant performance. Among 10 accessions intended to represent a range of heterozygosity levels and various essential oil chemotypes, the DKW–glucose growing medium generally produced the most vigorous plantlets by all parameters evaluated in vitro (height, biomass, canopy area, vegetative growth rate, and regeneration rate). Across four growing media treatments, all of which included meta-topolin as the sole plant growth regulator, poor to no rooting was observed in vitro. Hybrids were more vigorous than nonhybrid selections in vitro, but not in vivo. No correlation was observed between in vitro and in vivo vigor, indicating that, with these media, plant performance in vitro is not predictive of that in vivo.

Genome-wide association mapping of nutritional traits for designing superior chickpea varieties.

Micronutrient malnutrition is a serious concern in many parts of the world; therefore, enhancing crop nutrient content is an important challenge. Chickpea (Cicer arietinum L.), a major food legume crop worldwide, is a vital source of protein and minerals in the vegetarian diet. This study evaluated a diverse set of 258 chickpea germplasm accessions for 12 key nutritional traits. A significant variation was observed for several nutritional traits, including crude protein (16.56–24.64/100 g), β-Carotene (0.003–0.104 mg/100 g), calcium (60.69–176.55 mg/100 g), and folate (0.413–6.537 mg/kg). These data, combined with the available whole-genome sequencing data for 318,644 SNPs, were used in genome-wide association studies comprising single-locus and multi-locus models. We also explored the effect of varying the minor allele frequency (MAF) levels and heterozygosity. We identified 62 significant marker-trait associations (MTAs) explaining up to 28.63% of the phenotypic variance (PV), of which nine were localized within genes regulating G protein-coupled receptor signaling pathway, proteasome assembly, intracellular signal transduction, and oxidation–reduction process, among others. The significant effect MTAs were located primarily on Ca1, Ca3, Ca4, and Ca6. Importantly, varying the level of heterozygosity was found to significantly affect the detection of associations contributing to traits of interest. We further identified seven promising accessions (ICC10399, ICC1392, ICC1710, ICC2263, ICC1431, ICC4182, and ICC16915) with superior agronomic performance and high nutritional content as potential donors for developing nutrient-rich, high-yielding chickpea varieties. Validation of the significant MTAs with higher PV could identify factors controlling the nutrient acquisition and facilitate the design of biofortified chickpeas for the future.

Integrated Approach in Genomic Selection to Accelerate Genetic Gain in Sugarcane.

Marker-assisted selection (MAS) has been widely used in the last few decades in plant breeding programs for the mapping and introgression of genes for economically important traits, which has enabled the development of a number of superior cultivars in different crops. In sugarcane, which is the most important source for sugar and bioethanol, marker development work was initiated long ago; however, marker-assisted breeding in sugarcane has been lagging, mainly due to its large complex genome, high levels of polyploidy and heterozygosity, varied number of chromosomes, and use of low/medium-density markers. Genomic selection (GS) is a proven technology in animal breeding and has recently been incorporated in plant breeding programs. GS is a potential tool for the rapid selection of superior genotypes and accelerating breeding cycle. However, its full potential could be realized by an integrated approach combining high-throughput phenotyping, genotyping, machine learning, and speed breeding with genomic selection. For better understanding of GS integration, we comprehensively discuss the concept of genetic gain through the breeder’s equation, GS methodology, prediction models, current status of GS in sugarcane, challenges of prediction accuracy, challenges of GS in sugarcane, integrated GS, high-throughput phenotyping (HTP), high-throughput genotyping (HTG), machine learning, and speed breeding followed by its prospective applications in sugarcane improvement.

Assessment of Molecular Diversity and Heterozygosity in Corn (Zea mays L.) Inbred Lines Using Simple Sequence Repeat (SSR) Markers

In this study, polymerase chain reaction (PCR) was used to genotype 30 corn inbred lines using 32 simple sequence repeat (SSR) markers. The goal was to establish the level and pattern of genetic diversity as well as to define probable heterotic groups of corn inbred lines. The 32 SSR primers detected a total of 238 alleles in a total of 150 individuals analyzed. The mean different number of alleles, effective number of alleles, Shannon’s information index, plus observed (Ho) and expected (He) heterozygosity were estimated (Na = 1.33, Ne = 1.29, I = 0.21, Ho = 0.28, He = 0.15) – exhibiting the highest values for phi079 (Na = 2.00, Ne = 1.96, I = 0.68, Ho = 0.89, He = 0.49) and the lowest for phi050 (Na = 1.00, Ne = 1.00, I = 0.00, Ho = 0.00, He = 0.00). The mean values of Ho > He indicates that the population has a mating system avoiding inbreeding. The high level of overall observed heterozygosity in corn inbred lines (mean Ho = 0.28 > mean He = 0.15) may indicate greater allelic polymorphism present in these populations and the possible mixing of previously isolated materials in the germplasm collection. Polymorphism information content ranged from 0.79 (umc1109) to 0.25 (umc1143), with an overall average value of 0.37, indicating that the loci were moderately low to highly informative and could thus detect and quantify genetic diversity in the population studied. In our maize gene pool, total genetic differentiation is somewhat high (0.57), with an excess of homozygotes. Seventeen (17) SSR loci had negative fixation indices (F), indicating a significant heterozygosity level. The population genetic diversity indices were also computed based on the 30 populations analyzed. The Na, Ne, Shannon’s information index, Ho, and He varied from population S8L17 to S8L27 with mean values of 1.327, 1.293, 0.214, 0.284, and 0.151, respectively. Populations showed negative F values, indicating significantly higher heterozygosity, whereas polymorphic loci had a mean value of 32.71%. The estimated molecular variance among the corn population was 2.29 and 3.06 for the variance within populations with a total of 5.35. The results of AMOVA also revealed that genetic variation within individuals accounts for 57% of overall genetic diversity, whereas among populations variability accounts for 43%. The cluster analysis, population structure analysis, and principal coordinate analysis revealed the presence of two distinct subpopulations. As a result, the findings of this study provide a foundation for identifying heterotic groups and parental selection, providing a source of unique alleles for future maize breeding efforts.

Genomic Insights into Cultivated Mexican Vanilla planifolia Reveal High Levels of Heterozygosity Stemming from Hybridization.

Although vanilla is one of the most valuable spices, there is a lack of understanding of the genomic variability of the main vanilla producing species, Vanilla planifolia, within its cultivated origin, Mexico. High genomic heterozygosity levels within the globally cultivated ‘Daphna’ genome have raised questions on the possibility of a hybrid origin and analogous genomic signatures of vanilla cultivated within its origin. This study investigated these questions by assessing whether the genomic structure of Mexican V. planifolia reflected domestication events. Whole genome re-sequencing was used to compare genome complexity between 15 cultivated accessions from different regions and gene pools. Results showed high levels of heterozygosity, ranging from 2.48% to 2.85%, in all but one accession, which exhibited a low level (0.403%). Chromosome-level comparative analyses revealed genomic variability among samples, but no signals of chromosome rearrangements. These findings support the hypotheses that cultivated vanilla resulted from hybridization and that multiple domestication events have shaped cultivated vanilla leading to the formation of landraces. High cultural diversity within this region further supports the occurrence of multiple domestication processes. These results may help to improve breeding and conservation efforts aiming to preserve the genetic diversity of this beloved spice threatened by climate change.

ANALYSIS OF THE SPECIFICITY OF THE GENETIC STRUCTURE OF PADDLEFISH (POLYODON SPATHULA (WALBAUM, 1792)) USING ISSR MARKERS

Paddlefish (Polyodon spathula (WALBAUM, 1792)) is reared in aquaculture on Ukrainian farms as an alternative source of gourmet meat and caviar to compensate for the lack of this valuable sturgeon product, which was caused by a drastic reduction of sturgeon stocks in Ukraine's natural waters. However these stocks require analysis of the genetic structure of breeding material cultivated in the aquaculture of Ukraine for further control and maintainance of their polymorphism and heterogeneity. Genetic control will allow monitoring the condition of stocks, selection of the most acceptable source of breeding stock and optimizing the breeding of this object.
 The aim of the research was to determine the level of efficiency of the ISSR-PCR method for studying polymorphism and identifying specific features of the genetic structure of the paddlefish reared at fish farms in Ukraine. Materials and methods of research. The analysis was performed using two age groups of paddlefish (younger – age-4 and older – age-13–15), which were reared at the state institution "Production and Experimental Dnieper Sturgeon Breeding Plant named after Academician S.T. Artushchyk". Molecular genetic analysis was performed using three ISSR markers (B – (GAG)₆C; C – (AGC)₆G and E – (AGC)₆C) followed by separation of amplification products by agarose gel electrophoresis. The informativeness of ISSR primers was determined by such indicators as the effective multiplex ratio (EMR), marker index (MI), resolution (Rp), calculated according to the methods for dominant markers.
 Research results. The specifics of the genetic structure of the paddlefish of the Kherson stock were described using ISSR markers. The study showed that a total of 32 amplicons were obtained for the three primers, of which 87.5% were polymorphic. The largest number of amplicons was obtained using primer E – (AGC)₆C – 14 specimens, while primers B – (GAG)₆C and C – (AGC)₆G were observed 9 bands. The information polymorphism index (PIC) ranged from 0.227 (marker C) to 0.314 (marker E), with an average value of 0.256.
 The informativeness of the selected ISSR primers was assessed during the study of the paddlefish (mean values were: PIC = 0.256; PPB = 85.2%; EMR = 8.4; MI = 2.3; Rp = 9.7). These indicators demonstrated the level of informativeness and efficiency of selected intermicrosatellite loci for the analysis of polymorphisms of the genetic structure of the paddlefish. Marker E – (AGC)₆C had the highest values of PPB, PIC, EMR, MI and Rp compared to other selected ISSR-markers, which indicated the greatest effectiveness of this primer in population genetic studies of paddlefish.
 Ranges of amplicons at selected intermicrosatellite loci were determined: for marker B – (GAG)₆C from 215 to 1275 bp; for markers C – (AGC)₆G and E – (AGC)₆C in the range of 125–1265 bp and 320–1470 bp, respectively. Following monomorphic amplicons for all studied specimens of both age groups were determined: for marker C – allele 125, 245 and 395 bp; for marker B – (GAG)₆C – 1085 bp. Identified monomorphic bands in the future can be used for interspecific comparisons of different species and to establish the origin of samples.
 Differences between the studied different age groups of paddlefish were characterized, which consisted in: 1) the specificity of the frequency distribution of alleles encountered with high frequency (over 40%), 2) the absence of larger amplicons for markers B – (GAG)₆C and C – (AGC)₆G in older paddlefish groups and 3) the presence of different monomorphic alleles for marker E – (AGC)₆C (allele 380 bp in specimens of the younger and allele 320 bp in the older group). In the younger age group, a higher total number of amplified fragments (NTB) and the number of polymorphic fragments (NPB) were observed at the three loci studied compared to the older group.
 The biodiversity level according to the Shannon index I (0.394 ± 0.043 in the younger and 0.321 ± 0.043 in the older age group) and the level of heterozygosity (objective expected heterozygosity – 0.286 ± 0.034 and 0.231 ± 0.035, respectively) of the studied groups of paddlefish were determined.
 Conclusions. The obtained results demonstrated the effectiveness of the use of selected ISSR-markers to assess the polymorphism of the genetic structure of the otter, the state of biodiversity and the heterozygosity of stocks. The analysis performed by the ISSR-PCR method allowed characterizing the specifics of the genetic structure of the paddlefish and showing age differences. The obtained gene pool profile can be used as a basis for the certification of paddlefish stocks.

Genome sequencing of adapted diploid potato clones.

Cultivated potato is a vegetatively propagated crop, and most varieties are autotetraploid with high levels of heterozygosity. Reducing the ploidy and breeding potato at the diploid level can increase efficiency for genetic improvement including greater ease of introgression of diploid wild relatives and more efficient use of genomics and markers in selection. More recently, selfing of diploids for generation of inbred lines for F1 hybrid breeding has had a lot of attention in potato. The current study provides genomics resources for nine legacy non-inbred adapted diploid potato clones developed at Agriculture and Agri-Food Canada. De novo genome sequence assembly using 10× Genomics and Illumina sequencing technologies show the genome sizes ranged from 712 to 948 Mbp. Structural variation was identified by comparison to two references, the potato DMv6.1 genome and the phased RHv3 genome, and a k-mer based analysis of sequence reads showed the genome heterozygosity range of 1 to 9.04% between clones. A genome-wide approach was taken to scan 5 Mb bins to visualize patterns of heterozygous deleterious alleles. These were found dispersed throughout the genome including regions overlapping segregation distortions. Novel variants of the StCDF1 gene conferring earliness of tuberization were found among these clones, which all produce tubers under long days. The genomes will be useful tools for genome design for potato breeding.

Population genetic indices of veined Rapa whelk groups of the Black Sea remote regions

Abstract Genetic structure and genetic distance of Rapana venosa populations from remote regions of the Black Sea (Odessa Bay and eastern Crimea, Ukraine) were defined. Despite the significant difference in morphometric parameters, the investigated samples of mollusks are genetically very similar, and the distance between them is at the level of local populations. Common features of observed groups of Rapana in the northern part of the Black Sea are the unequal occurrence of some alleles and genotypes, a high level of heterozygosity and nonequilibrium in the Hardy-Weinberg equation. The gene flow is the most significant of the evolutionary factors that form the genetic structure of Rapana venosa populations.

Intra- and interspecific comparison of protein polymorphism to establish genetic differentiation in two sympatric species of Drosophila: D. bipectinata and D. malerkotliana.

Drosophila bipectinata species complex includes four monophyletic closely related sympatric species with perfect reproductive isolation in natural conditions. Among these, two species, i.e., D. bipectinata and D. malerkotliana are known to be more prevalent in their occurrence all along their distribution area of Oriental-Australian regions. Genetic characteristics of these two species have been studied by earlier researchers mainly by focusing on their chromosomal polymorphism to gain knowledge pertaining to their evolutionary trend. The present work is one step farther, as we considered isozyme variants of three polymorphic enzymes to envisage genetic differentiation among the different natural populations of these two species, along with, a comparative perusal of their certain population genetic parameters. Natural populations of these two species were sampled from eight places aligned on the north-south axis of India and were subjected to isozyme analysis. The collection of both species and the geographical locations were kept same to avoid the effect of temporal or seasonal factors on the distribution of their allelic frequency. The results of this study clearly indicate that there is intraspecific genetic structuring among the populations of both the species with a distinct steady increase in the level of heterozygosity from north to south. The evolutionary tree in the form of dendrogram depicts two genetically differentiated groups of natural populations, one for north and other for South India. Most essential aspect that has been noticed through this study is the evolutionary trend of these two sympatric species being largely similar all along the north-south axis of India.

Demographic, physiological and genetic factors linked to the poleward range expansion of the snail Nerita yoldii along the shoreline of China.

Species range shift is one of the most significant consequences of climate change in the Anthropocene. A comprehensive study, including demographic, physiological and genetic factors linked to poleward range expansion, is crucial for understanding how the expanding population occupies the new habitat. In the present study, we investigated the demographic, physiological and genetic features of the intertidal gastropod Nerita yoldii, which has extended its northern limit by ~200 km over the former biogeographical break of the Yangtze River Estuary in recent decades. Data from neutral single nucleotide polymorphisms (SNPs) showed that the new marginal populations formed a distinct cluster established by a few founders. Demographic modelling analysis revealed that the new marginal populations experienced a strong genetic bottleneck followed by recent demographic expansion. Successful expansion that overcame the founder effect might be attributed to its high capacity for rapid population growth and multiple introductions. According to the non-neutral SNPs under diversifying selection, there were high levels of heterozygosity in the new marginal populations, which might be beneficial for adapting to the novel thermal conditions. The common garden experiment showed that the new marginal populations have evolved divergent transcriptomic and physiological responses to heat stress, allowing them to occupy and survive in the novel environment. Lower transcriptional plasticity was observed in the new marginal populations. These results suggest a new biogeographical pattern of N. yoldii has formed with the occurrence of demographic, physiological and genetic changes, and emphasize the roles of adaptation of marginal populations during range expansion.

A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of "Genetic Purging" and Genomic Stability.

The Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus Neomonachus. The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in 1976 when the population was fewer than 1000 animals. Like other recovering species, the Hawaiian monk seal has been reported to have reduced genetic heterogeneity due to the bottleneck and subsequent inbreeding. Here, we report a chromosomal reference assembly for a male animal produced using a variety of methods. The final assembly consisted of 16 autosomes, an X, and portions of the Y chromosomes. We compared variants in this animal to other HMS and to a frequently sequenced human sample, confirming about 12% of the variation seen in man. To confirm that the reference animal was representative of the HMS, we compared his sequence to that of 10 other individuals and noted similarly low variation in all. Variation in the major histocompatibility (MHC) genes was nearly absent compared to the orthologous human loci. Demographic analysis predicts that Hawaiian monk seals have had a long history of small populations preceding the bottleneck, and their current low levels of heterozygosity may indicate specialization to a stable environment. When we compared our reference assembly to that of other species, we observed significant conservation of chromosomal architecture with other pinnipeds, especially other phocids. This reference should be a useful tool for future evolutionary studies as well as the long-term management of this species.

Research Progress on Genetic Basis of Fruit Quality Traits in Apple (Malus × domestica).

Identifying the genetic variation characteristics of phenotypic traits is important for fruit tree breeding. During the long-term evolution of fruit trees, gene recombination and natural mutation have resulted in a high degree of heterozygosity. Apple (Malus × domestica Borkh.) shows strong ecological adaptability and is widely cultivated, and is among the most economically important fruit crops worldwide. However, the high level of heterozygosity and large genome of apple, in combination with its perennial life history and long juvenile phase, complicate investigation of the genetic basis of fruit quality traits. With continuing augmentation in the apple genomic resources available, in recent years important progress has been achieved in research on the genetic variation of fruit quality traits. This review focuses on summarizing recent genetic studies on apple fruit quality traits, including appearance, flavor, nutritional, ripening, and storage qualities. In addition, we discuss the mapping of quantitative trait loci, screening of molecular markers, and mining of major genes associated with fruit quality traits. The overall aim of this review is to provide valuable insights into the mechanisms of genetic variation and molecular breeding of important fruit quality traits in apple.

Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding.

Single-cross maize hybrids display superior heterosis and are produced from crossing two parental inbred lines belonging to genetically different heterotic groups. Here we assembled 1,604 historically utilized maize inbred lines belonging to various female heterotic groups (FHGs) and male heterotic groups (MHGs), and conducted phenotyping and genomic sequencing analyses. We found that the FHGs and MHGs have undergone both convergent and divergent changes for different sets of agronomic traits. Using genome-wide selection scans and association analyses, we identified a large number of candidate genes that contributed to the improvement of agronomic traits of the FHGs and MHGs. Moreover, we observed increased genetic differentiation between the FHGs and MHGs across the breeding eras, and we found a positive correlation between increasing heterozygosity levels in the differentiated genes and heterosis in hybrids. Furthermore, we validated the function of two selected genes and a differentiated gene. This study provides insights into the genomic basis of modern hybrid maize breeding.