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Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds

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Journal of Animal Science and Biotechnology 2023年第3期14卷 887-907页

作者： Michael N.Romanov Alexandra S.Abdelmanova Vladimir I.Fisinin Elena A.Gladyr Natalia A.Volkova Olga A.Koshkina Andrey N.Rodionov Anastasia N.Vetokh Igor V.Gusev Dmitry V.Anshakov Olga I.Stanishevskaya Arsen V.Dotsev Darren K.Griffin Natalia A.Zinovieva L.K.Ernst Federal Research Centre for Animal Husbandry DubrovitsyPodolskMoscow RegionRussia School of Biosciences University of KentCanterburyUK Federal State Budget Scientific Institution Federal Research Centre“All-Russian Poultry Research and Technological Institute”of the Russian Academy of Sciences Sergiev PosadMoscow RegionRussia Breeding and Genetic Centre“Zagorsk Experimental Breeding Farm”–Branch of the Federal Research Centre“All-Russian Poultry Research and Technological Institute”of the Russian Academy of Sciences Sergiev PosadMoscow RegionRussia Russian Research Institute of Farm Animal Genetics and Breeding–Branch of the L.K.Ernst Federal Research Centre for Animal Husbandry St.PetersburgRussia

Background The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by,and formed due to,past and current admixture *** to diverse environments,including acclimation to harsh climatic conditions,has also left selection footprints in breed *** Using the Chicken 50K_CobbCons SNP chip,we genotyped four divergently selected breeds:two aboriginal,cold tolerant Ushanka and Orloff Mille Fleur,one egg-type Russian White subjected to artificial selection for cold tolerance,and one meat-type White *** of selective sweeps were determined in the studied breeds using three methods:(1)assessment of runs of homozygosity islands,(2)F_(ST) based population differential analysis,and(3)haplotype differentiation *** regions of true selection signatures were identified by two or more methods or in two or more *** these regions,we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other *** them,SOX5,ME3,ZNF536,WWP1,RIPK2,OSGIN2,DECR1,TPO,PPARGC1A,BDNF,MSTN,and beta-keratin genes can be especially mentioned as candidates for cold *** factors may be involved in regulating some of these important genes(e.g.,TPO and BDNF).Conclusion Based on a genome-wide scan,our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken *** include genes representing the sine qua non for adaptation to harsh *** tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals,and this warrants further investigation.

关键词： Acclimation Adaptation Chicken breeds Cold tolerance Divergent selection Genetic diversity Genomewide scan phenotypic traits Selective sweeps

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Cluster Analysis on Japonica Rice(Oryza sativa L.) with Good Eating Quality Based on SSR Markers and phenotypic traits

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Rice science 2010年第2期17卷 111-121页

作者： ZHANG Chun-hong LI Jin-zhou ZHU Zhen ZHANG Ya-dong ZHAO Ling WANG Cai-lin Institute of Food Crops/Jiangsu High Quality Rice R ＆ D Center/Nanjing Branch of Chinese National Center for Rice Improvement Jiangsu Academy of Agricultural Sciences Nanjing 210014 China College of Agriculture Nanjing Agricultural University Nanjing 210095 China

Diversity of 60 conventional japonica rice accessions with good eating quality at home and abroad was analyzed using SSR molecular markers, agronomic traits and taste characteristics. A total of 290 alleles were detected in the 60 accessions at 72 SSR loci with the high similarity coefficients varying between 0.600 and 0.924. The loci on chromosome 5 showed the greatest value in average allele number. Additionally, most of the SSR loci could detect 3 to 4 alleles. An UPGMA dendrogram based on the cluster analysis of the genetic similarity coefficients showed that the grouping trend of part of the rice accessions was geographic-related and most of the rice accessions in Jiangsu Province, China were clustered together. Furthermore, many domestic accessions from south and north origins in China were close to the foreign japonica rice varieties, as proved by their pedigree origin from the foreign high-quality sources. For taste characteristics, part of the accessions with excellent taste were clearly clustered into one category though they came from different geographical regions, which indicates that taste characteristics of some varieties were mainly genetically determined. In addition, the agronomic traits of japonica rice with good taste might be closely related with their geographical origins, but the relationship between superior taste characteristics and agronomic traits should be further clarified.

关键词： japonica rice simple sequence repeat marker cluster analysis phenotypic traits taste characteristics genetic diversity

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The Association Analysis of phenotypic traits and Elite Loci Sequencing in Spring Soybean

The Association Analysis of Phenotypic Traits and Elite Loci...

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2015中国遗传学会大会

作者：李强苏二虎王雪娇刘志雄高凤云内蒙古自治区农牧业科学院

We have studied the agronomic,yield and quality traits of 151 soybean accessions for 2 ***,CDDP and ISSR molecular markers were utilized in analyzing the relation between molecular markers and traits in order to ident... 详细信息

关键词： Soybean phenotypic traits Molecular markers Association analysis Sequencing

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Association analysis of phenotypic traits and elite loci sequencing in soybean

Association analysis of phenotypic traits and elite loci seq...

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第六届全国动植物数量遗传学学术研讨会

作者：李强高聚林张辉苏二虎内蒙古农牧业科学院内蒙古农业大学农学院

关键词： Soybean phenotypic traits Molecular markers Association analysis Sequencing

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phenotypic traits and Genetic Diversity of Erianthus arundinaceum Germplasm

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Agricultural Science & Technology 2015年第1期16卷 35-39页

作者：徐超华陆鑫马丽刘新龙刘洪博苏火生林秀琴蔡青云南省农业科学院甘蔗研究所云南开远661699 云南省甘蔗遗传改良重点实验室云南开远661699 云南省农业科学院生物技术与种质资源研究所云南昆明650223

[Objective] This study was conducted to utilize and estimate Erianthus arundinaceum resources and to develop their elite traits. [Method] phenotypic traits and genetic diversity were evaluated based on 5 quantitative traits and 21 qualitative traits of 162 accessions of Erianthus arundinaceum collected from nine provinces in China （74 in Yunnan, 15 in Fujian, 19 in Guizhou, 18 in Hainan, 14 in Sichuan, 10 in Jiangxi, 4 in Guangdong, 4 in Guangxi and 4 in Zhejiang）. [Result] The Shannon-Wiener indices of qualitative traits among the E. arundinaceum populations from different provinces were generally low. The accessions from Fujian exhibited the highest genetic diversity index （0.762 4）, while those from Guangxi showed the lowest one （0.294 2）. There were great genetic variances in quantitative traits, with mean variation coefficients ranging from 14.95% to 32.15%. The accessions from Yunnan showed the highest variation coefficient （32.15%） and those from Guangxi showed the lowest one （14.95%）. Brix exhibited extremely significant nega- tive correlation with altitude and plant height showed extremely significant negative correlation with latitude. Coefficients of genetic divergence indicated that a high proportion of total genetic variation was retained within the populations from different regions, and the high gene flow showed that there were active genetic exchanges among these populations, suggesting no significant genetic divergence among these populations. According to genetic distance and UPGMA, there was a certain correlation between genetic distance and different sampling regions of E. arundinaceum. [Conclusion] The results provide theoretical references for resource collection , het- erosis application and development of excellent genes of sugarcane germplasm.

关键词： Erianthus arundinaceum phenotypic traits Genetic diversity

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Correlation and path coefficient analysis for phenotypic traits of noble scallop Chlamys nobilis

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Marine Science Bulletin 2010年第2期12卷 55-60页

作者：李俊辉杜晓东邓岳文王庆恒广东海洋大学水产学院广东湛江524025

In April of 2006, a base population of the noble scallop Chlamys nobilis was established by collecting parental breeders from the stocks in Wushi, Zhanjiang. In December of 2006, 200 individuals were randomly sampled from the base population and subjected for correlation and path coefficient analysis. It was found that there were statistically significant phenotypic correlations among the traits （P 〈 0.01）. Total weight was significantly and positively correlated with the shell length （r = 0.934 3）, shell height （r = 0.895 9）, shell width （r = 0.899 1 ）, muscle weight （r = 0.882 0） and shell weight （r = 0.937 9）, respectively. Shell length, shell width, muscle weight, shell height and shell weight had positive and direct effects on the total weight, with values of 0.397 1, 0.321 9, 0.172 1, 0.089 6 and 0.066 9, respectively. Shell length, shell width and muscle weight had higher direct effects on the total weight than shell height and shell weight. A combined evaluation of correlation, direct effects and indirect effects showed that direct selection for shell length, shell width, muscle weight, shell height and shell weight would be effective to improving the total weight. It was concluded that these traits could be regarded as the selection criteria in breeding programs of the species.

关键词： Chlamys nobilis phenotypic traits correlation path coefficient analysis

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Genetic Diversity of Leaf phenotypic traits in Walnut Germplasm Resources

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Agricultural Science & Technology 2021年第1期22卷 1-8页

作者： YU Qiu-xiang LIU Jing LI Yang LIU Jin-li BAI Zhong-kui Changli Institute of Pomology Hebei Academy of Agricultural and Forestry SciencesChangli 066600PRC

In order to reveal the genetic diversity and variation sources of leaf phenotypic traits in walnut,the coefficient of variation,Shannon-weaver index,phenotypic differentiation coefficient,and the correlation of 9 leaf phenotypic traits for 251 walnut germplasm resources from two walnut populations were *** results showed that the averages of the variation coefficients and Shannon-weaver indexes of the leaf phenotype traits were 17.45%and 1.86 *** F values of most inter-population traits and all intra-population traits were highly significant,and the F values of inter-population leaf shape index,leaflet number,length and leaf length were very *** averages of inter-population and intra-population differentiation coefficients were 9.15%and 90.85%*** leaf size,leaf thickness,and leaflet number were highly correlated with trunk *** to the results of principal component analyses,the 9 traits can be simplified into four principal components,which represent leaf size,petiole,leaflet number and leaf shape,*** were extensive variations and rich genetic diversities in leaf phenotypic traits of walnut,and the intra-population variation was the leading source of phenotypic trait *** shape index,leaflet number,internode length and leaf length can be used for population *** size and thickness of leaves and the number of leaflets will affect the accumulation of nutrients in walnut tree,and then affect its trunk perimeter.

关键词： Walnut Leaf phenotypic traits Populations Diversity

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AoATG5 plays pleiotropic roles in vegetative growth,cell nucleus development,conidiation,and virulence in the nematode-trapping fungus Arthrobotrys oligospora

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Science China(Life Sciences) 2022年第2期65卷 412-425页

作者： Duanxu Zhou Yingmei Zhu Na Bai Le Yang Meihua Xie Jiangliu Yang Meichen Zhu Ke-Qin Zhang Jinkui Yang State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education Yunnan UniversityKunming 650091China School of Life Sciences Yunnan UniversityKunming 650091China

Autophagy is an evolutionarily conserved process in eukaryotes,which is regulated by autophagy-related genes(ATGs).Arthrobotrys oligospora is a representative species of nematode-trapping(NT)fungi that can produce special traps for nematode *** elucidate the biological roles of autophagy in NT fungi,we characterized an orthologous Atg protein,AoAtg5,in *** found that AoATG5 deletion causes a significant reduction in vegetative growth and conidiation,and that the transcript levels of several sporulation-related genes were significantly downregulated during sporulation *** addition,the cell nuclei were significantly reduced in theΔAoATG5 mutant,and the transcripts of several genes involved in DNA bio-synthesis,repair,and ligation were significantly ***ΔAoATG5 mutants,the autophagic process was significantly impaired,and trap formation and nematocidal activity were significantly *** transcriptome analysis results showed that AoAtg5 is involved in the regulation of multiple cellular processes,such as autophagy,nitrogen metabolism,DNA biosynthesis and repair,and vesicular *** summary,our results suggest that AoAtg5 is essential for autophagy and significantly contributes to vegetative growth,cell nucleus development,sporulation,trap formation,and pathogenicity in ***,thus providing a basis for future studies focusing on related mechanisms of autophagy in NT fungi.

关键词： Arthrobotrys oligospora autophagy-related gene AoATG5 phenotypic traits transcriptome analysis sporulation cell nucleus development

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Metabolic profiles and morphological characteristics of leaf tips among different sweet potato(Ipomoea batatas Lam.)varieties

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Journal of Integrative Agriculture 2024年第2期23卷 494-510页

作者： Wenqing Tan Xinbo Guo Zhangying Wang Rong Zhang Chaochen Tang Bingzhi Jiang Ruixue Jia Yuanyuan Deng Shaohai Yang Jingyi Chen Crops Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Crop Genetic Improvement of Guangdong ProvinceGuangzhou 510640China School of Food Science and Engineering South China University of TechnologyGuangzhou 510640China Sericultural&Agri-Food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional FoodsMinistry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products ProcessingGuangzhou 510610China

Sweet potato leaf tips have high nutritional value,and exploring the differences in the metabolic profiles of leaf tips among different sweet potato varieties can provide information to improve their *** this study,a UPLC-Q-Exactive Orbitrap/MS-based untargeted metabolomics method was used to evaluate the metabolites in leaf tips of 32 sweet potato *** varieties with distinct overall metabolic profiles(A01,A02,and A03),two varieties with distinct profiles of phenolic acids(A20 and A18),and three varieties with distinct profiles of flavonoids(A05,A12,and A16)were *** addition,a total of 163 and 29 differentially expressed metabolites correlated with the color and leaf shape of sweet potato leaf tips,respectively,were identified through morphological *** comparison analysis of the phenotypic traits and a metabolite-phenotypic trait correlation analysis indicated that the color differences of sweet potato leaf tips were markedly associated with ***,the level of polyphenols was correlated with the leaf shape of sweet potato leaf tips,with lobed leaf types having higher levels of polyphenols than the entire leaf *** findings on the metabolic profiles and differentially expressed metabolites associated with the morphology of sweet potato leaf tips can provide useful information for breeding sweet potato varieties with higher nutritional value.

关键词： sweet potato leaf tips phenotypic traits metabolic profile differentially expressed metabolites polyphenols

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Morphological and ISSR molecular markers reveal genetic diversity of wild hawthorns (Crataegus songorica K. Koch.) in Xinjiang, China

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Journal of Integrative Agriculture 2017年第11期16卷 2482-2495页

作者： SHENG Fang CHEN Shu-ying TIAN Jia LI Peng QIN Xue WANG Lei LUO Shu-ping LI Jiang College of Forestry and Horticulture Xinjiang Agricultural University Urumqi 830052 P.R. China Academy of Forestry in Ili Yining 835000 P.R. China Zhengzhou Fruit Research Institute Chinese Academy of Agricultural Sciences Zhengzhou 450009 P.R. China

The wild hawthorn species, Crataegus songorica K. Koch., is an important wild germplasm resource in Xinjiang, China that has been endangered in recent years. The genetic diversity of C. songorica K. Koch. germplasm in five populations from Daxigou, Xinjiang, China were evaluated based on phenotypic traits and ISSR molecular markers to provide basic infor- mation on resource protection, rational utilization and genetic improvement. The F-value for the phenotypic differentiation coefficient of the 33 traits measured ranged from 0.266 to 15.128, and mean value was 13.85%. The variation among populations was found to be lower than that within population. A total of 303 loci were detected within the five populations by 12 primers. Within 298,polymorphic loci, the polymorphism was 98.35%, showing a high genetic diversity in C. songorica K. Koch. The gene diversity within population, total population genetic diversity, genetic differentiation coefficient and gene flow were 0.2779, 0.3235, 0.1408, and 3.0511, respectively. Our results showed that C. songorica K. Koch. from Xinjiang has a high level of genetic diversity at both the phenotypic and molecular levels. Significant genetic differentiation existed within population and the differentiation trend showed a regional association. And in this study, in situ and ex situ conser- vation approaches were raised for wild hawthorn protection utilization.

关键词： phenotypic traits ISSR marker genetic diversity Crataegus songorica K. Koch. germplasm resources molecular marker

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