BMC Genetics最新文献

{"title":"Genetic stability, genetic variation, and fitness performance of the genetic sexing Salaya1 strain for Bactrocera dorsalis, under long-term mass rearing conditions.","authors":"Nidchaya Aketarawong,&nbsp;Siriwan Isasawin,&nbsp;Kamoltip Laohakieat,&nbsp;Sujinda Thanaphum","doi":"10.1186/s12863-020-00933-4","DOIUrl":"https://doi.org/10.1186/s12863-020-00933-4","url":null,"abstract":"<p><strong>Background: </strong>A genetic sexing strain (GSS) is an essential component for pest control using the sterile insect technique (SIT). A GSS is developed using a combination of Y-autosome translocation and a selectable marker such as pupal color, resulting in heterozygous males and homozygous females that possess wild-type brown pupae (wp⁺) and mutant white pupae (wp) alleles, respectively. The genetic sexing Salaya1 strain developed for Bactrocera dorsalis was evaluated using a clean stream and scaled-up for subsequent production lines (e.g., initiation, injection, and release). Colony management under small- and large-scale conditions for long-term rearing may affect the sexing system, genetic background, and fitness performance of the strain. Routine monitoring was applied to study genetic stability, genetic variation, and male mating competitiveness.</p><p><strong>Results: </strong>The percentage of recombinants was significantly different between males (wp) and females (wp⁺), ranging between 0.21-0.43% and 0.01-0.04%, respectively. Using 106 bands from six ISSR markers, the genetic backgrounds of two generations (F₄₀ and F₁₀₈) of the clean stream were found to be almost identical (0.960), and between those two generations and the wild population, the similarities were 0.840 and 0.800, respectively. In addition, the sterile males performed well in competitive mating with fertile females (Relative Sterility Index = 0.67 ± 0.13). The rates of fliers calculated from both clean and release streams were higher than 0.95. Regarding the fitness of the Salaya1 strain, the fertility and pupal recovery were similar in all production lines. The sex ratio (Male/Female) distortion was also recorded.</p><p><strong>Conclusions: </strong>The Salaya1 strain reared at the mass-rearing facility retained its genetic stability, genetic variation, behavior (e.g., competitive mating and flight ability), and traits related to fitness for at least 10 consecutive generations. The filter rearing system is effective at minimising the selection pressure while maintaining the genetic background and fitness performances of the clean stream. These characteristics were stable throughout the production lines. In addition, the production efficiency is comparable among the different production lines and other similar types of GSSs.</p>","PeriodicalId":9197,"journal":{"name":"BMC Genetics","volume":"21 Suppl 2","pages":"131"},"PeriodicalIF":2.9,"publicationDate":"2020-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12863-020-00933-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38729965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and characterization of a pupal-colour based genetic sexing strain of Anastrepha fraterculus sp. 1 (Diptera: Tephritidae).","authors":"José S Meza,&nbsp;Kostas Bourtzis,&nbsp;Antigone Zacharopoulou,&nbsp;Angeliki Gariou-Papalexiou,&nbsp;Carlos Cáceres","doi":"10.1186/s12863-020-00932-5","DOIUrl":"https://doi.org/10.1186/s12863-020-00932-5","url":null,"abstract":"<p><strong>Background: </strong>Area-wide integrated pest management programs (AW-IPM) incorporating sterile insect technique (SIT) have been successful in suppressing populations of different fruit fly species during the last six decades. In addition, the development of genetic sexing strains (GSS) for different fruit fly species has allowed for sterile male-only releases and has significantly improved the efficacy and cost effectiveness of the SIT applications. The South American Fruit Fly Anastrepha fraterculus (Diptera: Tephritidae) is a major agricultural pest attacking several fruit commodities. This impedes international trade and has a significant negative impact on the local economies. Given the importance of sterile male-only releases, the development of a GSS for A. fraterculus would facilitate the implementation of an efficient and cost-effective SIT operational program against this insect pest species.</p><p><strong>Results: </strong>For potential use in a GSS, three new morphological markers (mutants) were isolated in a laboratory strain of A. fraterculus sp. 1, including the black pupae (bp) gene located on chromosome VI. The black pupa phenotype was used as a selectable marker to develop genetic sexing strains by linking the wild type allele (bp⁺) to the Y-chromosome -via irradiation to induce a reciprocal Y-autosome translocation. Four GSS were established and one of them, namely GSS-89, showed the best genetic stability and the highest fertility. This strain was selected for further characterization and cytogenetic analysis.</p><p><strong>Conclusions: </strong>We herein report the development of the first genetic sexing strain of a major agricultural pest, A. fraterculus sp. 1, using as a selectable marker the black pupae genetic locus.</p>","PeriodicalId":9197,"journal":{"name":"BMC Genetics","volume":"21 Suppl 2","pages":"134"},"PeriodicalIF":2.9,"publicationDate":"2020-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12863-020-00932-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38727851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Climate stress resistance in male Queensland fruit fly varies among populations of diverse geographic origins and changes during domestication.","authors":"Ángel-David Popa-Báez,&nbsp;Siu Fai Lee,&nbsp;Heng Lin Yeap,&nbsp;Shirleen S Prasad,&nbsp;Michele Schiffer,&nbsp;Roslyn G Mourant,&nbsp;Cynthia Castro-Vargas,&nbsp;Owain R Edwards,&nbsp;Phillip W Taylor,&nbsp;John G Oakeshott","doi":"10.1186/s12863-020-00935-2","DOIUrl":"https://doi.org/10.1186/s12863-020-00935-2","url":null,"abstract":"<p><strong>Background: </strong>The highly polyphagous Queensland fruit fly (Bactrocera tryoni Froggatt) expanded its range substantially during the twentieth century and is now the most economically important insect pest of Australian horticulture, prompting intensive efforts to develop a Sterile Insect Technique (SIT) control program. Using a \"common garden\" approach, we have screened for natural genetic variation in key environmental fitness traits among populations from across the geographic range of this species and monitored changes in those traits induced during domestication.</p><p><strong>Results: </strong>Significant variation was detected between the populations for heat, desiccation and starvation resistance and wing length (as a measure of body size). Desiccation resistance was correlated with both starvation resistance and wing length. Bioassay data for three resampled populations indicate that much of the variation in desiccation resistance reflects persistent, inherited differences among the populations. No latitudinal cline was detected for any of the traits and only weak correlations were found with climatic variables for heat resistance and wing length. All three stress resistance phenotypes and wing length changed significantly in certain populations with ongoing domestication but there was also a strong population by domestication interaction effect for each trait.</p><p><strong>Conclusions: </strong>Ecotypic variation in heat, starvation and desiccation resistance was detected in Australian Qfly populations, and these stress resistances diminished rapidly during domestication. Our results indicate a need to select source populations for SIT strains which have relatively high climatic stress resistance and to minimise loss of that resistance during domestication.</p>","PeriodicalId":9197,"journal":{"name":"BMC Genetics","volume":"21 Suppl 2","pages":"135"},"PeriodicalIF":2.9,"publicationDate":"2020-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12863-020-00935-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38390012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Precise single base substitution in the shibire gene by CRISPR/Cas9-mediated homology directed repair in Bactrocera tryoni.","authors":"Amanda Choo,&nbsp;Elisabeth Fung,&nbsp;Isabel Y Chen,&nbsp;Robert Saint,&nbsp;Peter Crisp,&nbsp;Simon W Baxter","doi":"10.1186/s12863-020-00934-3","DOIUrl":"https://doi.org/10.1186/s12863-020-00934-3","url":null,"abstract":"<p><strong>Background: </strong>Pest eradication using the Sterile Insect Technique (SIT) involves high-density releases of sterilized males that mate with wild females and ultimately suppress the population. Sterilized females are not required for SIT and their removal or separation from males prior to release remains challenging. In order to develop genetic sexing strains (GSS), conditional traits such as temperature sensitive lethality are required.</p><p><strong>Results: </strong>Here we introduce a known Drosophila melanogaster temperature sensitive embryonic lethal mutation into Bactrocera tryoni, a serious horticultural pest in Australia. A non-synonymous point mutation in the D. melanogaster gene shibire causes embryonic lethality at 29 °C and we successfully used CRISPR/Cas9 technology to recreate the orthologous shibire temperature sensitive-1 (shi^ts1) mutation in B. tryoni. Genotypic analyses over three generations revealed that a high fitness cost was associated with the shi^ts1 mutant allele and shi^ts1 homozygotes were not viable at 21 °C, which is a more severe phenotype than that documented in D. melanogaster.</p><p><strong>Conclusions: </strong>We have demonstrated the first successful use of CRISPR/Cas9 to introduce precise single base substitutions in an endogenous gene via homology-directed repair in an agricultural pest insect and this technology can be used to trial other conditional mutations for the ultimate aim of generating genetic sexing strains for SIT.</p>","PeriodicalId":9197,"journal":{"name":"BMC Genetics","volume":"21 Suppl 2","pages":"127"},"PeriodicalIF":2.9,"publicationDate":"2020-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12863-020-00934-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38390013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeted generation of polyploids in Hydrangea macrophylla through cross-based breeding.","authors":"Conny Tränkner,&nbsp;Kristina Günther,&nbsp;Peter Sahr,&nbsp;Frauke Engel,&nbsp;Annette Hohe","doi":"10.1186/s12863-020-00954-z","DOIUrl":"https://doi.org/10.1186/s12863-020-00954-z","url":null,"abstract":"<p><strong>Background: </strong>Up to now, diploid and triploid cultivars were reported for the ornamental crop Hydrangea macrophylla. Especially, the origin of triploids and their crossing behaviors are unknown, but the underlying mechanisms are highly relevant for breeding polyploids.</p><p><strong>Results: </strong>By screening a cultivar collection, we identified diploid, triploid, tetraploid and even aneuploid H. macrophylla varieties. The pollen viability of triploids and tetraploids was comparable to that of diploids. Systematic crosses with these cultivars resulted in viable diploid, triploid, tetraploid and aneuploid offspring. Interestingly, crosses between diploids produced diploid and 0 or 1-94% triploid offspring, depending on the cultivars used as pollen parent. This finding suggests that specific diploids form unreduced pollen, either at low or high frequencies. In contrast, crosses of triploids with diploids or tetraploids produced many viable aneuploids, whose 2C DNA contents ranged between the parental 2C values. As expected, crosses between diploid and tetraploid individuals generated triploid offspring. Putative tetraploid plants were obtained at low frequencies in crosses between diploids and in interploid crosses of triploids with either diploid or tetraploid plants. The analysis of offspring populations indicated the production of 1n = 2x gametes for tetraploid plants, whereas triploids produced obviously reduced, aneuploid gametes with chromosome numbers ranging between haploid and diploid level. While euploid offspring grew normally, aneuploid plants showed mostly an abnormal development and a huge phenotypic variation within offspring populations, most likely due to the variation in chromosome numbers. Subsequent crosses with putative diploid, triploid and aneuploid offspring plants from interploid crosses resulted in viable offspring and germination rates ranging from 21 to 100%.</p><p><strong>Conclusions: </strong>The existence of diploids that form unreduced pollen and of tetraploids allows the targeted breeding of polyploid H. macrophylla. Different ploidy levels can be addressed by combining the appropriate crossing partners. In contrast to artificial polyploidization, cross-based polyploidization is easy, cheap and results in genetically variable offspring that allows the direct selection of more robust and stress tolerant polyploid varieties. Furthermore, the generation of polyploid H. macrophylla plants will favor interspecific breeding programs within the genus Hydrangea.</p>","PeriodicalId":9197,"journal":{"name":"BMC Genetics","volume":" ","pages":"147"},"PeriodicalIF":2.9,"publicationDate":"2020-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12863-020-00954-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38685193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin.","authors":"Mariano Joly Kpatènon,&nbsp;Kolawolé Valère Salako,&nbsp;Sylvain Santoni,&nbsp;Leila Zekraoui,&nbsp;Muriel Latreille,&nbsp;Christine Tollon-Cordet,&nbsp;Cédric Mariac,&nbsp;Estelle Jaligot,&nbsp;Thierry Beulé,&nbsp;Kifouli Adéoti","doi":"10.1186/s12863-020-00955-y","DOIUrl":"https://doi.org/10.1186/s12863-020-00955-y","url":null,"abstract":"<p><strong>Background: </strong>In Sub-Saharan Africa, Borassus aethiopum Mart. (African fan palm) is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity and population structure of B. aethiopum across nine collection sites spanning the three climatic regions of Benin, West Africa, through the use of microsatellite markers.</p><p><strong>Results: </strong>During a first phase we relied on the reported transferability of primers developed in other palm species. We find that, in disagreement with previously published results, only 22.5% of the markers tested enable amplification of B. aethiopum DNA and polymorphism detection is very low. In a second phase, we generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the de novo detection of microsatellite loci. Among the primer pairs targeting these, 11 detected polymorphisms and were further used for analyzing genetic diversity. Across the nine sites, expected heterozygosity (He) ranges from 0.263 to 0.451 with an overall average of 0.354, showing a low genetic diversity. Analysis of molecular variance (AMOVA) shows that within-site variation accounts for 53% of the genetic variation. Accordingly, the low number of migrants and positive values of the fixation index (F) in sites from both the Central (Sudano-Guinean) and the Southern (Guinean) climatic regions suggest limited gene flow between sites. The global correlation between genetic and geographic distances is weak; however, our clustering analyses indicate that B. aethiopum palms from Savè (Center) are genetically more similar to those from the North than to samples from other Central sites.</p><p><strong>Conclusions: </strong>In the light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic diversity analyses targeting under-studied species, and suggest future applications for our molecular resources. We propose that, while prominent short-range pollen and seed dispersal in Benin explain most of our results, gene flux between the Central and Northern regions, as a result of animal and/or human migrations, might underlie the Savè discrepancy.</p>","PeriodicalId":9197,"journal":{"name":"BMC Genetics","volume":" ","pages":"145"},"PeriodicalIF":2.9,"publicationDate":"2020-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12863-020-00955-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38670809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improving the accuracy of genomic evaluation for linear body measurement traits using single-step genomic best linear unbiased prediction in Hanwoo beef cattle.","authors":"Masoumeh Naserkheil, Deuk Hwan Lee, Hossein Mehrban","doi":"10.1186/s12863-020-00928-1","DOIUrl":"10.1186/s12863-020-00928-1","url":null,"abstract":"<p><strong>Background: </strong>Recently, there has been a growing interest in the genetic improvement of body measurement traits in farm animals. They are widely used as predictors of performance, longevity, and production traits, and it is worthwhile to investigate the prediction accuracies of genomic selection for these traits. In genomic prediction, the single-step genomic best linear unbiased prediction (ssGBLUP) method allows the inclusion of information from genotyped and non-genotyped relatives in the analysis. Hence, we aimed to compare the prediction accuracy obtained from a pedigree-based BLUP only on genotyped animals (PBLUP-G), a traditional pedigree-based BLUP (PBLUP), a genomic BLUP (GBLUP), and a single-step genomic BLUP (ssGBLUP) method for the following 10 body measurement traits at yearling age of Hanwoo cattle: body height (BH), body length (BL), chest depth (CD), chest girth (CG), chest width (CW), hip height (HH), hip width (HW), rump length (RL), rump width (RW), and thurl width (TW). The data set comprised 13,067 phenotypic records for body measurement traits and 1523 genotyped animals with 34,460 single-nucleotide polymorphisms. The accuracy for each trait and model was estimated only for genotyped animals using five-fold cross-validations.</p><p><strong>Results: </strong>The accuracies ranged from 0.02 to 0.19, 0.22 to 0.42, 0.21 to 0.44, and from 0.36 to 0.55 as assessed using the PBLUP-G, PBLUP, GBLUP, and ssGBLUP methods, respectively. The average predictive accuracies across traits were 0.13 for PBLUP-G, 0.34 for PBLUP, 0.33 for GBLUP, and 0.45 for ssGBLUP methods. Our results demonstrated that averaged across all traits, ssGBLUP outperformed PBLUP and GBLUP by 33 and 43%, respectively, in terms of prediction accuracy. Moreover, the least root of mean square error was obtained by ssGBLUP method.</p><p><strong>Conclusions: </strong>Our findings suggest that considering the ssGBLUP model may be a promising way to ensure acceptable accuracy of predictions for body measurement traits, especially for improving the prediction accuracy of selection candidates in ongoing Hanwoo breeding programs.</p>","PeriodicalId":9197,"journal":{"name":"BMC Genetics","volume":" ","pages":"144"},"PeriodicalIF":2.9,"publicationDate":"2020-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7709290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38666687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic analysis of rice seedling traits related to machine transplanting under different seeding densities.","authors":"Dan Zhu,&nbsp;Yuping Zhang,&nbsp;Jing Xiang,&nbsp;Yaliang Wang,&nbsp;Defeng Zhu,&nbsp;Yikai Zhang,&nbsp;Huizhe Chen","doi":"10.1186/s12863-020-00952-1","DOIUrl":"https://doi.org/10.1186/s12863-020-00952-1","url":null,"abstract":"<p><strong>Background: </strong>Due to the diversity of rice varieties and cropping systems in China, the limitation of seeding density and seedling quality makes it hard to improve machine-transplanted efficiency. Previous studies have shown that indica and japonica varieties varied in machine transplanting efficiency and optimal seeding density. In this study, a RIL population derived from '9311' and 'Nipponbare' were performed to explore the seedling traits variations and the genetic mechanism under three seeding densities.</p><p><strong>Results: </strong>The parents and RIL population exhibited similar trends as the seeding density increased, including seedling height and first leaf sheath length increases, shoot dry weight and root dry weight decreases. Among the 37 QTLs for six traits detected under the three seeding densities, 12 QTLs were detected in both three seeding densities. Five QTL hotspots identified clustered within genomic regions on chromosomes 1, 2, 4, 6 and 11. Specific QTLs such as qRDW_1.1 and qFLSL_5.1 were detected under low and high seeding densities, respectively. Detailed analysis the QTL regions identified under specific seeding densities revealed several candidate genes involved in phytohormones signals and abiotic stress responses. Whole-genome additive effects showed that '9311' contributed more loci enhancing trait performances than 'Nipponbare', indicating '9311' was more sensitive to the seeding density than 'Nipponbare'. The prevalence of negative epistasis effects indicated that the complementary two-locus homozygotes may not have marginal advantages over the means of the two parental genotypes.</p><p><strong>Conclusions: </strong>Our results revealed the differences between indica rice and japonica rice seedling traits in response to seeding density. Several QTL hotspots involved in different traits and specific QTLs (such as qRDW_1.1 and qFLSL_5.1) in diverse seeding densities had been detected. Genome-wide additive and two-locus epistasis suggested a dynamic of the genetic control underlying different seeding densities. It was concluded that novel QTLs, additive and epistasis effects under specific seeding density would provide adequate information for rice seedling improvement during machine transplanting.</p>","PeriodicalId":9197,"journal":{"name":"BMC Genetics","volume":" ","pages":"133"},"PeriodicalIF":2.9,"publicationDate":"2020-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12863-020-00952-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38646896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identifying rare variants for quantitative traits in extreme samples of population via Kullback-Leibler distance.","authors":"Yang Xiang,&nbsp;Xinrong Xiang,&nbsp;Yumei Li","doi":"10.1186/s12863-020-00951-2","DOIUrl":"https://doi.org/10.1186/s12863-020-00951-2","url":null,"abstract":"<p><strong>Background: </strong>The rapid development of sequencing technology and simultaneously the availability of large quantities of sequence data has facilitated the identification of rare variant associated with quantitative traits. However, existing statistical methods depend on certain assumptions and thus lacking uniform power. The present study focuses on mapping rare variant associated with quantitative traits.</p><p><strong>Results: </strong>In the present study, we proposed a two-stage strategy to identify rare variant of quantitative traits using phenotype extreme selection design and Kullback-Leibler distance, where the first stage was association analysis and the second stage was fine mapping. We presented a statistic and a linkage disequilibrium measure for the first stage and the second stage, respectively. Theory analysis and simulation study showed that (1) the power of the proposed statistic for association analysis increased with the stringency of the sample selection and was affected slightly by non-causal variants and opposite effect variants, (2) the statistic here achieved higher power than three commonly used methods, and (3) the linkage disequilibrium measure for fine mapping was independent of the frequencies of non-causal variants and simply dependent on the frequencies of causal variants.</p><p><strong>Conclusions: </strong>We conclude that the two-stage strategy here can be used effectively to mapping rare variant associated with quantitative traits.</p>","PeriodicalId":9197,"journal":{"name":"BMC Genetics","volume":" ","pages":"130"},"PeriodicalIF":2.9,"publicationDate":"2020-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12863-020-00951-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38638198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association studies for methane emission and ruminal volatile fatty acids using Holstein cattle sequence data.","authors":"Ali Jalil Sarghale,&nbsp;Mohammad Moradi Shahrebabak,&nbsp;Hossein Moradi Shahrebabak,&nbsp;Ardeshir Nejati Javaremi,&nbsp;Mahdi Saatchi,&nbsp;Majid Khansefid,&nbsp;Younes Miar","doi":"10.1186/s12863-020-00953-0","DOIUrl":"https://doi.org/10.1186/s12863-020-00953-0","url":null,"abstract":"<p><strong>Background: </strong>Methane emission by ruminants has contributed considerably to the global warming and understanding the genomic architecture of methane production may help livestock producers to reduce the methane emission from the livestock production system. The goal of our study was to identify genomic regions affecting the predicted methane emission (PME) from volatile fatty acids (VFAs) indicators and VFA traits using imputed whole-genome sequence data in Iranian Holstein cattle.</p><p><strong>Results: </strong>Based on the significant-association threshold (p < 5 × 10^- 8), 33 single nucleotide polymorphisms (SNPs) were detected for PME per kg milk (n = 2), PME per kg fat (n = 14), and valeric acid (n = 17). Besides, 69 genes were identified for valeric acid (n = 18), PME per kg milk (n = 4) and PME per kg fat (n = 47) that were located within 1 Mb of significant SNPs. Based on the gene ontology (GO) term analysis, six promising candidate genes were significantly clustered in organelle organization (GO:0004984, p = 3.9 × 10^- 2) for valeric acid, and 17 candidate genes significantly clustered in olfactory receptors activity (GO:0004984, p = 4 × 10^- 10) for PME traits. Annotation results revealed 31 quantitative trait loci (QTLs) for milk yield and its components, body weight, and residual feed intake within 1 Mb of significant SNPs.</p><p><strong>Conclusions: </strong>Our results identified 33 SNPs associated with PME and valeric acid traits, as well as 17 olfactory receptors activity genes for PME traits related to feed intake and preference. Identified SNPs were close to 31 QTLs for milk yield and its components, body weight, and residual feed intake traits. In addition, these traits had high correlations with PME trait. Overall, our findings suggest that marker-assisted and genomic selection could be used to improve the difficult and expensive-to-measure phenotypes such as PME. Moreover, prediction of methane emission by VFA indicators could be useful for increasing the size of reference population required in genome-wide association studies and genomic selection.</p>","PeriodicalId":9197,"journal":{"name":"BMC Genetics","volume":" ","pages":"129"},"PeriodicalIF":2.9,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12863-020-00953-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38729866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}