Retention Of Allele Research Articles

Construction and Evaluation of Pepper Core Collection Based on Phenotypic Traits and SSR Markers

To streamline germplasm preservation, enhance resource utilization, and improve breeding efficiency, a core germplasm bank was established using 24 phenotypic traits and DNP markers from 155 pepper resources across various regions. Selection of the optimal core germplasm was based on intra-group retention ratio, overall retention scale, and intra-group stepwise clustering retention. Evaluation of phenotypic trait data for the core germplasm utilized mean, variance, range, and coefficient of variation, with principal component analysis confirming the selection. For molecular evaluation, the core germplasm pre-selection plan was based on SSR clustering, allele retention ratio, and Shannon-Weaver diversity index. This approach resulted in a core germplasm of 41 resources, including 6 var. fasciculatum, 7 var. grossum, 3 var. cerasiorme, 6 var. conoides, and 19 var. longum, representing the maximum phenotypic retention and genetic diversity of the 155 pepper resources. Additionally, a core germplasm of 32 resources was generated based on SSR markers, retaining all 54 polymorphic loci. By integrating phenotypic and molecular core collections, a combined core collection of 57 varieties was developed. This collection achieved a 92.55% phenotype retention ratio and a 100% polymorphism site retention ratio. With a 90% compression ratio, it encapsulates the broad genetic diversity of the original germplasm, serving as a comprehensive resource for further research and breeding applications.

Parental Polymorphism Survey for Identifying Genes/QTLs for BPH Resistance in Assam Land Race 10-3

The current research was taken up at Institute of Biotechnology (IBT), PJTSAU, Hyderabad Telangana, India in kharif from August to November, 2021 to access the parental polymorphism between 10-3 and Telangana Sona. 10-3, an Assam landrace, is a bold grain rice variety with high BPH resistance to biotype-4. Whereas, Telangana Sona (RNR 15048) is a short and slender grain variety of rice that is popular among farmers and consumers across Telangana and other Indian states due to its high yield and low glycemic index. Despite being blast resistant, Telangana Sona is susceptible to the insect pest Brown Plant hopper (BPH) Nilaparvata lugens (Stål). The present study aimed to characterize the parental polymorphism between 10–3 and Telangana sona to facilitate mapping of genetic loci linked with BPH resistance in the 10–3 and to optimize the retention of favourable alleles from Telangana sona during marker assisted backcross breeding. Eight hundred and sixteen highly variable Simple Sequence Repeats (SSRs) including thirty-five BPH linked markers covering 12 chromosomes were used to assess DNA polymorphism between 10-3 and Telangana Sona. Out of 816 markers screened, 97 (11.89%) were found to be polymorphic between 10–3 and Telangana Sona of which, 82 were genomic SSRs and 15 were BPH linked markers. Chromosome 6 exhibited highest polymorphism percentage with a value of 30%, indicating that this chromosome is useful in studying parental variation and lowest polymorphism percentage found on chromosome 5 (3.49%). These 97 polymorphic markers will help in construction of linkage map for identifying QTLs linked with BPH resistance and for marker assisted backcrossing breeding in Telangana Sona.

Functional significance of asymmetrical retention of parental alleles in a hybrid pine species complex

AbstractHybrid genomes usually harbor asymmetrical parental contributions. However, it is challenging to infer the functional significance of asymmetrical retention of parental alleles in hybrid populations of conifer trees. Here we investigated the diversity in the glutathione S‐transferase (GST) gene family in a hybrid pine Pinus densata and its parents (Pinus tabuliformis and Pinus yunnanensis). Plant GSTs play major roles in protecting plants against biotic and abiotic stresses. In this study, 19 orthologous groups of GST genes were identified and cloned from these three species. We examined their expression in different tissues, and then purified the corresponding proteins to characterize their enzymatic activities and specificities toward different substrates. We found that among the 19 GST orthologous groups, divergence in gene expression and in enzymatic activities toward different substrates was prevalent. P. densata preferentially retained P. yunnanensis‐like GSTs for 17 out of the 19 gene loci. We determined the first GST crystal structure from conifer species at a resolution of 2.19 Å. Based on this structure, we performed site‐directed mutagenesis to replace amino acid residuals in different wild‐types of GSTs to understand their functional impacts. Reciprocal replacement of amino acid residuals in native GSTs of P. densata and P. tabuliformis demonstrated significant changes in enzyme functions and identified key sites controlling GSTs activities. This study illustrates an approach to evaluating the functional significance of sequence variations in conifer genomes. Our study also sheds light on plausible mechanisms for controlling the selective retention of parental alleles in the P. densata genome.

Indication-specific tumor evolution and its impact on neoantigen targeting and biomarkers for individualized cancer immunotherapies

BackgroundIndividualized neoantigen-specific immunotherapy (iNeST) requires robustly expressed clonal neoantigens for efficacy, but tumor mutational heterogeneity, loss of neoantigen expression, and variable tissue sampling present challenges. It is assumed that clonal...

Applying Population Viability Analysis to Inform Genetic Rescue That Preserves Locally Unique Genetic Variation in a Critically Endangered Mammal

Genetic rescue can reduce the extinction risk of inbred populations, but it has the poorly understood risk of ‘genetic swamping’—the replacement of the distinctive variation of the target population. We applied population viability analysis (PVA) to identify translocation rates into the inbred lowland population of Leadbeater’s possum from an outbred highland population that would alleviate inbreeding depression and rapidly reach a target population size (N) while maximising the retention of locally unique neutral genetic variation. Using genomic kinship coefficients to model inbreeding in Vortex, we simulated genetic rescue scenarios that included gene pool mixing with genetically diverse highland possums and increased the N from 35 to 110 within ten years. The PVA predicted that the last remaining population of lowland Leadbeater’s possum will be extinct within 23 years without genetic rescue, and that the carrying capacity at its current range is insufficient to enable recovery, even with genetic rescue. Supplementation rates that rapidly increased population size resulted in higher retention (as opposed to complete loss) of local alleles through alleviation of genetic drift but reduced the frequency of locally unique alleles. Ongoing gene flow and a higher N will facilitate natural selection. Accordingly, we recommend founding a new population of lowland possums in a high-quality habitat, where population growth and natural gene exchange with highland populations are possible. We also recommend ensuring gene flow into the population through natural dispersal and/or frequent translocations of highland individuals. Genetic rescue should be implemented within an adaptive management framework, with post-translocation monitoring data incorporated into the models to make updated predictions.

Genetic Variation and Population Differentiation in the Bovine Lymphocyte Antigen DRB3.2 Locus of South African Nguni Crossbred Cattle.

Simple SummaryIndigenous cattle breeds are important to their native environment as they confer significant and often unique adaptability traits. The Nguni is one such breeds that is indigenous to the Southern African region. This breed confers resistance to thermal stress and diseases, amongst other factors. The bovine major histocompatibility complex is an important region, which codes for alleles that have been associated with a plethora of diseases. In the current study, the genetic diversity within this region was assessed in Nguni crossbred cattle. This was done to detect the gene pool of the Nguni breed, and to identify genes that might be important within this breed. The populations displayed a high degree of genetic diversity, and some alleles were common throughout the populations and accounted for a significant portion of the total alleles. This high genetic diversity could account for the great adaptability of the Nguni breed to Southern Africa. The bovine lymphocyte antigen (BoLA-DRB3) gene is an important region that codes for glycoproteins responsible for the initiation of an immune response. BoLA-DRB3 alleles have been demonstrated to be associated with disease resistance/tolerance. Therefore, great genetic diversity is correlated with better adaptation, fitness, and robustness. The current study was conducted to assess the population genetic structure of the BoLA-DRB3 gene in Nguni crossbred cattle using polymerase chain reaction-sequence based typing (PCR-SBT). High genetic diversity was detected, with 30 alleles, 11 of which are novel to the study. Alleles DRB3*0201, DRB3*0701, DRB*0901, and DRB*1601 were present in all populations and accounted for nearly around 50% of all observed alleles. A mean genetic diversity (HE) of 0.93 was detected. The high overall genetic diversity is possibly associated with pathogen-assisted selection and heterozygote advantage. Such high diversity might explain the hardiness of the Nguni crossbred cattle to the Southern African region. Low population genetic structure was identified (FST = 0.01), suggesting possible gene flow between populations and retention of similar alleles. The study was undertaken to bridge the dearth of such studies in South African breeds and it is imperative for effective sustainability of indigenous breeds and the implementation of effective breeding strategies.

Patterns of chromosome 18 loss of heterozygosity in multifocal ileal neuroendocrine tumors.

Ileal neuroendocrine tumors (NETs) represent the most common neoplasm of the small intestine. Although up to 50% of patients with ileal NETs are diagnosed with multifocal disease, the mechanisms by which multifocal ileal NETs arise are not yet understood. In this study, we analyzed genome‐wide sequencing data to examine patterns of copy number variation in 40 synchronous primary ileal NETs derived from three patients. Chromosome (chr) 18 loss of heterozygosity (LOH) was the most frequent copy number alteration identified; however, not all primary tumors from the same patient had evidence of this LOH. Our data revealed three distinct patterns of chr18 allelic loss, indicating that primary tumors from the same patient can present different LOH patterns including retention of either parental allele. In conclusion, our results are consistent with the model that multifocal ileal NETs originate independently. In addition, they suggest that there is no specific germline allele on chr18 that is the target of somatic LOH.

Development of Laos Khao Kai Noi rice landrace (Oryza sativa L.) core collection as a model for rice genetic resources management in the Laos National Genebank

Khao Kai Noi rice is considered as an elite quality landrace in Laos, which has led to its germplasm conservation in the Laos National Genebank. As happens with other germplasm collections, a manageable yet representative sub collection has become an essential element for researchers and breeders to simplify many activities, including those related to crop improvement, phenotype-genotype correlation and determination of diversity hotspots. In this study, 109 accessions were used as a test collection for core collection development to determine the feasibility of collection reduction in a closely related rice group. Three core collections were developed by two established methodologies and evaluated by diversity indexes, allele retention, phylogenetic distribution and geographical location. Based on SSR molecular markers and PowerCore, a reduction to 24 accessions was achieved with the conservation of complete genetic diversity. A K-means based on reduction to 24 accessions rendered slightly lesser results while based on 12 accessions resulted in a 17% diversity loss. These core collections may be useful for genebank management, research and breeding activities in the future. Also, they may as well serve to estimate core collection development behavior in other landraces and cultivars, which is fundamental in genetic resources management and utilization.

Balancing act: modelling sustainable release numbers for translocations

AbstractTranslocated populations often share demographic, environmental and genetic risks associated with relict populations. Models that predict translocation impacts on source and founder populations are therefore necessary to ensure that harvesting for release does not jeopardize either population. However, current models generally focus on maximizing the long‐term demographic viability and retention of allelic diversity in the founder population only. We therefore risk estimating a release number that is considered ‘appropriate' for maintaining viability and allelic diversity in the founder population but is in fact detrimental to the source. Our objectives were to determine a sustainable number of individuals for release that maximized the viability and allelic diversity of source and founder populations. We developed a spatially explicit individual‐based model that simulated hypothetical translocation scenarios for the threatened New Zealand frog, Leiopelma pakeka, which was restricted to Te Hoiere/Maud Island and has been heavily targeted for translocations. Source and translocated populations were simulated over 200 generations, representing 200 years across various initial population sizes from 20 to 300 frogs. To account for the potential loss of allelic diversity from the source population via harvesting, along with genetic drift and founder events typically associated with translocations, an additional set of simulations determined the probability of retaining a single diploid locus within populations with rare and common alleles. Our results showed that at least 120 frogs were required for populations to remain viable and maximize allelic retention in the long‐term, regardless of allelic diversity. However, harvesting more than 150 frogs led to ongoing or the onset of declines in the viability and allelic retention of source populations. We recommend that future translocations of L. pakeka harvest no more than 140 frogs from each of the sub‐populations on Te Hoiere/Maud Island. We also recommend the described approach to simulate hypothetical translocation scenarios for other managed species.

The Influence of Selection on MHC DQA and DQB Haplotypes in the Endemic New Zealand Hector's and Māui Dolphins.

Strong balancing selection on the major histocompatibility complex (MHC) can lead to different patterns in gene frequencies and neutral genomic variation within species. We investigated diversity and geographic structure of MHC genes DQA and DQB, as well as their inferred functional haplotypes, from 2 regional populations (East and West Coast) of the endangered Hector's dolphin (Cephalorhynchus hectori hectori) and the critically endangered Māui dolphin (Cephalorhynchus hectori maui) (West Coast, North Island), and contrasted these results with patterns from neutral microsatellites. The Māui had the lowest number of alleles for DQA (2) and DQB (3), consistent with strong genetic drift acting on this remnant population. However, the 2 retained DQA alleles are among the most divergent combinations of all 4 alleles found across the Hector's metapopulation, potentially reflecting the retention of divergent alleles due to balancing selection. The high frequency of the divergent DQB*04 allele also gave this population the highest nucleotide diversity for DQB. Strong differentiation was evident for DQA, DQB, and DQA-DQB haplotypes between the regional populations of Hector's dolphins (FST > 0.213) and both subspecies (FST > 0.311). Differentiation was generally greater than observed at neutral microsatellite loci, suggesting the influence of selection between geographically proximate East and West Coast populations. This might be the result of spatial differences in directional selection on those opposite coastlines. In addition, measures of the ratio of nonsynonymous to synonymous substitutions (dN/dS) were consistent with balancing selection over evolutionary time. Together, these results suggest a complex interplay of balancing selection, directional selection, local fidelity, and genetic drift.

Genetic diversity, core collection and breeding history of Pleurotus ostreatus in China

Abstract Pleurotus ostreatus is one of the most widespread and favourably cultivated mushrooms in China. The cultivated strains of this species have been frequently exchanged domestically and internationally, but no detailed breeding history has been documented. The frequent domestic and international exchange of strains combined with a non-detailed historical documentation of breeding might have led to confusion about strain names and genetic background. In this study, 91 strains of P. ostreatus, including 57 cultivated and 34 wild strains, were analysed using 21 simple sequence repeat markers developed from the genomic sequence of “P. cf. floridanus”. Among the cultivated strains, 46 were found to possess different allelic patterns. The remaining 11 strains were clustered into five groups, each with their own private alleles, suggesting that 10.5% (6/57) of the cultivated strains were previously labelled with improper names. Our analyses indicate that wild strains harbored greater genetic diversity than the cultivated strains. With regard to the cultivation history of P. ostreatus, the cultivated strains in China have three sources: direct introduction from Europe, domestication from wild strains from China, or hybridisation of the European and Chinese strains. Furthermore, we propose a core collection of P. ostreatus with 34 strains, including 13 wild and 21 cultivated strains. The allele retention proportion of the core collection for the entire collection was 100%.

Segregation distortion and genome-wide digenic interactions affect transmission of introgressed chromatin from wild cotton species

This study reports transmission genetics of chromosomal segments into Gossypium hirsutum from its most distant euploid relative, Gossypium mustelinum . Mutilocus interactions and structural rearrangements affect introgression and segregation of donor chromatin. Wild allotetraploid relatives of cotton are a rich source of genetic diversity that can be used in genetic improvement, but linkage drag and non-Mendelian transmission genetics are prevalent in interspecific crosses. These problems necessitate knowledge of transmission patterns of chromatin from wild donor species in cultivated recipient species. From an interspecific cross, Gossypium hirsutum × Gossypium mustelinum, we studied G. mustelinum (the most distant tetraploid relative of Upland cotton) allele retention in 35 BC3F1 plants and segregation patterns in BC3F2 populations totaling 3202 individuals, using 216 DNA marker loci. The average retention of donor alleles across BC3F1 plants was higher than expected and the average frequency of G. mustelinum alleles in BC3F2 segregating families was less than expected. Despite surprisingly high retention of G. mustelinum alleles in BC3F1, 46 genomic regions showed no introgression. Regions on chromosomes 3 and 15 lacking introgression were closely associated with possible small inversions previously reported. Nonlinear two-locus interactions are abundant among loci with single-locus segregation distortion, and among loci originating from one of the two subgenomes. Comparison of the present results with those of prior studies indicates different permeability of Upland cotton for donor chromatin from different allotetraploid relatives. Different contributions of subgenomes to two-locus interactions suggest different fates of subgenomes in the evolution of allotetraploid cottons. Transmission genetics of G. hirsutum × G. mustelinum crosses reveals allelic interactions, constraints on fixation and selection of donor alleles, and challenges with retention of introgressed chromatin for crop improvement.

Genetic diversity and structure of core collection of winter mushroom (Flammulina velutipes) developed by genomic SSR markers

BackgroundA core collection is a subset of an entire collection that represents as much of the genetic diversity of the entire collection as possible. The establishment of a core collection for crops is practical for efficient management and use of germplasm. However, the establishment of a core collection of mushrooms is still in its infancy, and no established core collection of the economically important species Flammulina velutipes has been reported.ResultsWe established the first core collection of F. velutipes, containing 32 strains based on 81 genetically different F. veltuipes strains. The allele retention proportion of the core collection for the entire collection was 100%. Moreover, the genetic diversity parameters (the effective number of alleles, Nei’s expected heterozygosity, the number of observed heterozygosity, and Shannon’s information index) of the core collection showed no significant differences from the entire collection (p > 0.01). Thus, the core collection is representative of the genetic diversity of the entire collection. Genetic structure analyses of the core collection revealed that the 32 strains could be clustered into 6 groups, among which groups 1 to 3 were cultivars and groups 4 to 6 were wild strains. The wild strains from different locations harbor their own specific alleles, and were clustered stringently in accordance with their geographic origins. Genetic diversity analyses of the core collection revealed that the wild strains possessed greater genetic diversity than the cultivars.ConclusionWe established the first core collection of F. velutipes in China, which is an important platform for efficient breeding of this mushroom in the future. In addition, the wild strains in the core collection possess favorable agronomic characters and produce unique bioactive compounds, adding value to the platform. More attention should be paid to wild strains in further strain breeding.

Genetic Population Structure across the Range of Endangered Northeastern Bulrush,Scirpus ancistrochaetus

Premise of research. Determining population structure and the spatial distribution of existing genetic variation is important for prioritizing areas for conservation of endangered species. Specifically, identifying clusters of genetically differentiated populations ensures that the genetic diversity of a species is conserved. Scirpus ancistrochaetus, northeastern bulrush, is a federally endangered wetland sedge, found in eight states in the northeastern United States, for which little information on genetic structure is available.Methodology. We collected leaf samples from 96 separate wetlands spanning seven states and representing over half of all known sites (N = 71 sites). We sequenced eight variable loci, which were used to construct distance-based trees and calculate population-assignment probabilities to investigate population structure, and we tested isolation by distance by correlating genetic similarity with geographic distance among populations.Pivotal results. All plants sampled from the same wetland (i.e., a population) were genetically identical with low heterozygosity, and there was little to no variation among clustered wetlands within a site. Scirpus ancistrochaetus was genetically structured across its range. Notably, all populations from New England were genetically identical to each other but differed from all other populations, and a similar pattern was observed for northern Pennsylvania populations. Three genetic clusters were identified, including a primarily New England cluster, a primarily Pennsylvanian cluster, and a southern Appalachian cluster, and overall, genetic distances were consistent with isolation by distance. Although genetic clusters mostly corresponded with geography, some populations did not show this geographic-genetic association, suggesting long-distance dispersal; for example, one population from West Virginia was assigned to the New England cluster. Overall, the highest genetic diversity was found within Pennsylvania and nearby states.Conclusions. Whether similarity between geographically distant locations is due to animal-mediated gene flow or retention of ancestral alleles needs additional study. Additionally, the development of a large number of new markers may help to reveal diversity in areas such as New England with wetlands that did not have any diversity using our markers. Nevertheless, conservation of different genetic clusters at a regional scale is important for maintaining the genetic diversity of S. ancistrochaetus, particularly in its southern range, where the greater amount of genetic diversity suggests that this region is a reservoir of genetic variation.

Selective Retention of an Inactive Allele of the DKK2 Tumor Suppressor Gene in Hepatocellular Carcinoma.

In an effort to identify the functional alleles associated with hepatocellular carcinoma (HCC), we investigated 152 genes found in the 4q21-25 region that exhibited loss of heterozygosity (LOH). A total of 2,293 pairs of primers were designed for 1,449 exonic and upstream promoter regions to amplify and sequence 76.8–114 Mb on human chromosome 4. Based on the results from analyzing 12 HCC patients and 12 healthy human controls, we discovered 1,574 sequence variations. Among the 99 variants associated with HCC (p < 0.05), four are from the Dickkopf 2 (DKK2) gene: three in the promoter region (g.-967A>T, g.-923C>A, and g.-441T>G) and one in the 5’UTR (c.550T>C). To verify the results, we expanded the subject cohort to 47 HCC cases and 88 healthy controls for conducting haplotype analysis. Eight haplotypes were detected in the non-tumor liver tissue samples, but one major haplotype (TAGC) was found in the tumor tissue samples. Using a reporter assay, this HCC-associated allele registered the lowest level of promoter activity among all the tested haplotype sequences. Retention of this allele in LOH was associated with reduced DKK2 transcription in the HCC tumor tissues. In HuH-7 cells, DKK2 functioned in the Wnt/β-catenin signaling pathway, as an antagonist of Wnt3a, in a dose-dependent manner that inhibited Wnt3a-induced cell proliferation. Taken together, the genotyping and functional findings are consistent with the hypothesis that DKK2 is a tumor suppressor; by selectively retaining a transcriptionally inactive DKK2 allele, the reduction of DKK2 function results in unchecked Wnt/β-catenin signaling, contributing to HCC oncogenesis. Thus our study reveals a new mechanism through which a tumor suppressor gene in a LOH region loses its function by allelic selection.

Population structure and core collection construction of apricot (Prunus armeniacaL.) in North Africa based on microsatellite markers

North Africa enclosed original apricot genetic resources with the cohabitation of grafting and seed-propagated accessions. In this study, we assessed the genetic diversity and population structure of 183 apricot accessions using 24 microsatellite markers distributed evenly in thePrunusgenome. A total of 192 alleles and a high level of gene diversity (0.593) were detected among the whole panel. Genetic structure analysis revealed the presence of four genetic clusters. We also found that both geographical origin and mode of propagation are important factors structuring genetic diversity in apricot species. Results confirmed the presence of gene exchange between the northern and southern countries of the Mediterranean Basin. Subsequently, a core collection of 98 accessions based on M (maximization) strategy showing 99.47% of allele retention ratio was constructed. No significant differences for Shannon's information index and Nei's diversity index were observed between the core and entire collections. Our results provide an effective aid for future germplasm preservation and conservation strategies as well as genetic association studies development in relation to phenotypic data.

Copy number alterations and allelic ratio in relation to recurrence of rectal cancer.

BackgroundIn rectal cancer, total mesorectal excision surgery combined with preoperative (chemo)radiotherapy reduces local recurrence rates but does not improve overall patient survival, a result that may be due to the harmful side effects and/or co-morbidity of preoperative treatment. New biomarkers are needed to facilitate identification of rectal cancer patients at high risk for local recurrent disease. This would allow for preoperative (chemo)radiotherapy to be restricted to high-risk patients, thereby reducing overtreatment and allowing personalized treatment protocols. We analyzed genome-wide DNA copy number (CN) and allelic alterations in 112 tumors from preoperatively untreated rectal cancer patients. Sixty-six patients with local and/or distant recurrent disease were compared to matched controls without recurrence. Results were validated in a second cohort of tumors from 95 matched rectal cancer patients. Additionally, we performed a meta-analysis that included 42 studies reporting on CN alterations in colorectal cancer and compared results to our own data.ResultsThe genomic profiles in our study were comparable to other rectal cancer studies. Results of the meta-analysis supported the hypothesis that colon cancer and rectal cancer may be distinct disease entities. In our discovery patient study cohort, allelic retention of chromosome 7 was significantly associated with local recurrent disease. Data from the validation cohort were supportive, albeit not statistically significant, of this finding.ConclusionsWe showed that retention of heterozygosity on chromosome 7 may be associated with local recurrence in rectal cancer. Further research is warranted to elucidate the mechanisms and effect of retention of chromosome 7 on the development of local recurrent disease in rectal cancer.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1550-0) contains supplementary material, which is available to authorized users.

Presize: an approach for precise estimation of core collection size using the Similarity Elimination (SimEli) method

Core collections are the integral part of biotechnology-aided modern-day crop improvement programmes and utilized for a variety of applications including conventional plant breeding, association mapping, resequencing, among others. Since their advent, determination of core collection size has been based on the size of the whole collection. In this study, we precisely estimated the size of the core collection based on the diversity of the whole collection using the Similarity Elimination method. For each of the elimination cycle, allele retention and pairwise and mean genetic distances were calculated and used as the criteria for the precise estimation of the core collection size. We sampled a coconut core collection with 266 entries by retaining the diversity of the whole collection. During the elimination process, accessions with very rare alleles were eliminated first when compared with those having rare and common alleles. Therefore, our results support the hypothesis that the less frequent alleles seldom contribute to the genetic distance when compared with common alleles. In conclusion, presize can be efficiently utilized in any crop for the precise estimation of core collection size.

Differential requirement of GRP94 and GRP78 in mammary gland development.

Glucose Regulated Protein (GRP) 94 and GRP78 are critical molecular chaperones and regulators of signaling. Conditional knockout mouse models have revealed tissue specific requirements for GRP94 and GRP78, including selection for allele retention in specific cell types. Here we report the consequences of mammary-targeted knockout of these GRPs. Our studies revealed that MMTV-Cre, Grp94f/f mammary glands, despite GRP94 deficiency, exhibited normal proliferation and ductal morphogenesis. Interestingly, MMTV-Cre, Grp78f/f mammary glands displayed only slightly reduced GRP78 protein levels, associating with the retention of the non-recombined Grp78 floxed alleles in isolated mammary epithelial cells and displayed phenotypes comparable to wild-type glands. In contrast, transduction of isolated Grp78f/f mammary epithelial stem/progenitor cells with adenovirus expressing GFP and Cre-recombinase was successful in GRP78 ablation, and the GFP sorted cells failed to give rise to repopulated mammary glands in de-epithelialized recipient mice. These studies imply GRP78, but not GRP94, is required for mammary gland development.

Simulating Retention of Rare Alleles in Small Populations to Assess Management Options for Species with Different Life Histories

Preserving allelic diversity is important because it provides the capacity for adaptation and thus enables long-term population viability. Allele retention is difficult to predict in animals with overlapping generations, so we used a new computer model to simulate retention of rare alleles in small populations of 3 species with contrasting life-history traits: North Island Brown Kiwi (Apteryx mantelli; monogamous, long-lived), North Island Robins (Petroica longipes; monogamous, short-lived), and red deer (Cervus elaphus; polygynous, moderate lifespan). We simulated closed populations under various demographic scenarios and assessed the amounts of artificial immigration needed to achieve a goal of retaining 90% of selectively neutral rare alleles (frequency in the source population = 0.05) after 10 generations. The number of immigrants per generation required to meet the genetic goal ranged from 11 to 30, and there were key similarities and differences among species. None of the species met the genetic goal without immigration, and red deer lost the most allelic diversity due to reproductive skew among polygynous males. However, red deer required only a moderate rate of immigration relative to the other species to meet the genetic goal because nonterritorial breeders had a high turnover. Conversely, North Island Brown Kiwi needed the most immigration because the long lifespan of locally produced territorial breeders prevented a large proportion of immigrants from recruiting. In all species, the amount of immigration needed generally decreased with an increase in carrying capacity, survival, or reproductive output and increased as individual variation in reproductive success increased, indicating the importance of accurately quantifying these parameters to predict the effects of management. Overall, retaining rare alleles in a small, isolated population requires substantial investment of management effort. Use of simulations to explore strategies optimized for the populations in question will help maximize the value of this effort..