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Telomere-to-telomere genome assembly of melon(Cucumis melo L.var.inodorus)provides a high-quality reference for meta-QTL analysis of important traits

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Horticulture Research 2023年第10期10卷 202-214页

作者： Minghua Wei Ying Huang Changjuan Mo Haiyan Wang Qingguo Zeng Wenli Yang Jihao Chen Xuejun Zhang Qiusheng Kong National Key Laboratory for Germplasm Innovation&Utilization of Horticultural Crops College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan 430070China Hami-melon Research Center Xinjiang Academy of Agricultural SciencesUrumqi 830091China Hainan Sanya Experimental Center for Crop Breeding Xinjiang Academy of Agricultural SciencesSanya 572014China

Melon is an important horticultural crop with extensive diversity in many horticultural groups.To explore its genomic diversity,it is necessary to assemble more high-quality complete genomes from different melon accessions.Meanwhile,a large number of QTLs have been mapped in several studies.Integration of the published QTLs onto a complete genome can provide more accurate information for candidate gene cloning.To address these problems,a telomere-to-telomere(T2T)genome of the elite melon landrace Kuizilikjiz(Cucumis melo L.var.inodorus)was de novo assembled and all the published QTLs were projected onto it in this study.The results showed that a high-quality Kuizilikjiz genome with the size of 379.2 Mb and N50 of 31.7 Mb was de novo assembled using the combination of short reads,PacBio high-fidelity long reads,Hi-C data,and a high-density genetic map.Each chromosome contained the centromere and telomeres at both ends.A large number of structural variations were observed between Kuizilikjiz and the other published genomes.A total of 1294 QTLs published in 67 studies were collected and projected onto the T2T genome.Several clustered,co-localized,and overlapped QTLs were determined.Furthermore,20 stable meta-QTLs were identified,which significantly reduced the mapping intervals of the initial QTLs and greatly facilitated identification of the candidate genes.Collectively,the T2T genome assembly together with the numerous projected QTLs will not only broaden the high-quality genome resources but also provide valuable and abundant QTL information for cloning the genes controlling important traits in melon.

关键词： Cucumis elite traits

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Selection of Suitable Area and Analysis of Adaptability Difference of Prunus humilis

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Asian Agricultural Research 2024年第3期16卷 41-45页

作者： Ze YAO Shengxiu JIANG Zizhu YAN Qi WANG Dawei WANG Gansu Desert Control Research Institute Lanzhou 730700China Gansu Psammophytes Engineering Technology Research Center Lanzhou 730700China State Key Laboratory of Desertification and Aeolian Sand Disaster Combating Lanzhou 730700China

This paper delves into and assesses the differences in biological traits and fruit nutritional composition of 3 varieties of Prunus humilis introduced from 2 different regions.Results showed that(i)the contents of protein,total sugar,and calcium of No.5 variety were higher those of the other 2 varieties,which was recognized as the most suitable variety for fresh fruit;(ii)the comparison of leaf areas index and fruit shape index of 3 varieties shows that the fruit shape index and individual fruit weight of the introduced varieties were higher than those of the control,the diameter of individual fruit of the introduced varieties higher than that of the control indicated that they had a higher fruit hardness,more dry matter accumulation and better fruit quality,and that the introduction region was more suitable for scale-up of P.humilis;(iii)there was a positive correlation with the number of fruiting branches and there was a significant negative correlation with individual fruit weight,while the leaf area had a significant negative correlation with the number of fruiting branches.The introduced varieties can develop normally in the 2 testing areas,notably,No.5 variety performed better than No.4 and No.6.Improving management is the prerequisite for maintaining proper number of fruiting branches and high yield.

关键词： Prunus humilis Biological traits Nutritional components Introduction and cultivation

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Integrating genome-wide association study with multi-tissue transcriptome analysis provides insights into the genetic architecture of teat traits in pigs

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Journal of Genetics and Genomics 2023年第10期50卷 795-798页

作者： Chen Wei Xiaodian Cai Shuqi Diao Jinyan Teng Zhiting Xu Wenjing Zhang Haonan Zeng Zhanming Zhong Xibo Wu Yahui Gao Jiaqi Li Zhe Zhang State Key Laboratory of Swine and Poultry Breeding Industry Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular BreedingCollege of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdong 510642China Guangxi State Farms Yongxin Animal Husbandry Group Co.Ltd. NanningGuangxi 530022China

Porcine teat numbers are crucial indicators of the reproductive performance of sows in the pig industry.During lactation periods,sows with fewer teats may lead to inadequate colostrum intake in piglets,which affects piglet weight gain and mortality(Tummaruk,2013).In pig breeding,high-intensity artificial selection on litter traits potentially gives rise to the functional weakening of teat traits due to the pleiotropic effects of genes affecting both traits(Chen et al.,2022).

关键词： breeding traits artificial

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Genetic Dissection of Quantitative Trait Loci for Panicle traits and Heat Tolerance by High-Density Bin Map in Rice

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Rice science 2022年第6期29卷 507-511,I0007-I0020页

作者： LIU Hongyan MA Xiaosong LI Enxi ZENG Xianjun LUO Lijun Shanghai Agrobiological Gene Center Shanghai 201106China Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization Ministry of Agriculture and Rural AffairsShanghai 201106China Hainan University Haikou 570228China Huazhong Agricultural University Wuhan 430070China

A recombinant inbred line(RIL)with 179 lines derived from a cross between a heat tolerant line Huhan 1B and a heat sensitive line Hanhui 3 was used for QTL mapping for panicle traits and heat tolerance.A total of 52 QTLs were identified with LOD scores from 3.85 to 54.93,each explaining 0.70%to 21.48%of the phenotypic variances,including 11 for panicle length(PL),11 for seed number per panicle(SN),14 for spikelet number per panicle(SNPP),6 for seed-setting rate(SSR)under normal conditions,and 5 for seed-setting rate(SSR_HT)and 5 for relative seed-setting rate(RSSR)under heat stress,respectively.

关键词： panicle traits Map

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Additive Effects of QTLs/Genes on Rice Grain Size traits Revealed by Genetic Comparisons

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Rice science 2023年第3期30卷 171-175,I0002-I0013页

作者： HE Lei LIANG Wenhua HU Jiang ZHAO Chunfang YAO Shu CHEN Tao ZHU Zhen ZHAO Qingyong LU Kai ZHAO Ling ZHOU Lihui QIAN Qian WANG Cailin ZHANG Yadong Institute of Food Crops Jiangsu Academy of Agricultural Science/Key Laboratory of Jiangsu Province for Agrobiology/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River(Nanjing)Ministry of Agriculture and Rural AffairsNanjing 210014China East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice Nanjing 210014China State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 311400China

Grain size is controlled by many QTLs and/or genes.Despite intensive study,the genetic interactions between these QTLs/genes remain largely unclear.We previously found that the japonica large-grain rice cultivar TD70 with 1000-grain weight of 68.6 g carries superior alleles at the loci GW2,GS3,qGL3,GS5 and GW8,all of which are known to control grain size,while the indica rice variety Kasalath with 1000-grain weight of 19.1 g has normal alleles at these loci.

关键词： cultivar alleles traits

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Postharvest Variations of Rice Physicochemical traits and Volatile Compounds under Granary Conditions During Long-Time Storage

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Rice science 2023年第2期30卷 92-95,I0007-I0009页

作者： HU Hao LIU Xingquan HE Yukai JIN Jiande WU Fenghua HUANG Shiwen ZHANG Jiaojiao College of Food and Health Zhejiang Agriculture and Forest UniversityHangzhou 311300China China National Rice Research Institute Hangzhou 310006China Zhejiang Province Grain Reserve Management Co.LTD Hangzhou 310006China

Rice quality is influenced by many factors,viz.,temperature,humidity,atmosphere and storage time.To uncover quality variations of rice after postharvest,we estimated the physicochemical properties and volatile compounds of an indica rice Zhongzheyou 8 under granary conditions(20ºC-25ºC in summer and 10ºC-15ºC in other seasons)for three years.

关键词： traits humidity harvest

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Geographic variation in growth and wood traits of Neolamarckia cadamba in China

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Forestry Research 2022年第1期2卷 121-131页

作者： Qingmin Que Kunxi Ouyang Chunmei Li Buye Li Huiyun Song Pei Li Ruiqi Pian Huaqing Li Xiaoyang Chen Changcao Peng College of Forestry and Landscape Architecture Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmSouth China Agricultural UniversityWushan Road 483Tianhe DistrictGuangzhou 510642P.R.China China Forestry Group Leizhou Forestry Bureau Co. Ltd.Zhanjiang 524348GuangdongP.R.China State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources South China Agricultural UniversityWushan Road 483Tianhe DistrictGuangzhou 510642P.R.China

Neolamarckia cadamba is an indigenous,timber-producing tree species in Southern China that plays an important role in the sustainable development of the local forestry industry.However,the geographic genetic variation across its natural distribution area in Southern China has yet to be characterized for best utilization.Here,we report the geographic genetic variation in growth and wood properties of N.cadamba from 10 provenances that represent the entire natural distribution of N.cadamba in Southern China.There was significant geographic variation in diameter breast height(DBH),height(H),volume(V),vessel length(VL),vessel diameter(VD),VL/VD,and wood basic density(WBD).The variation in tree volume across provenances was greater than that of other growth traits,indicating that volume has a greater potential for selection in provenance trials.The provenance heritabilities of growth traits and wood properties ranged from 0.59 to 0.67 and from 0.40 to 0.45,respectively.Trend surface analysis revealed that patterns of geographic variation associated with growth traits were weakly negatively correlated with those of wood properties.The pattern of geographic variation in growth traits showed a gradual increase from the periphery to the central region,whereas wood properties showed the opposite pattern,and latitude had the greatest effect on both.Wood property measurements suggested that the YNMS provenance produced superior timber wood,whereas the GXLZ,GXFCG,and GXNN provenances produced the best pulpwood.These provenances could potentially provide more valuable breeding materials for the genetic improvement of N.cadamba.

关键词： breeding traits pattern

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Sex ratio, floral traits, and genetic variation of androdioecious Osmanthus fragrans L. (Oleaceae) and the implications for maintenance of high male frequency

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Ornamental Plant Research 2022年第1期2卷 230-236页

作者： Lihua Zhou Liyuan Yang Qiu Fang Bin Dong Yiguang Wang Shiwei Zhong Zheng Xiao Hongbo Zhao Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants School of Landscape and ArchitectureZhejiang A&F UniversityHangzhou 311300ZhejiangChina

Several examples of androdioecy appear to have evolved from dioecy and have low male frequency(<0.5).However,the evolutionary pathway to androdioecy in Oleaceae may come from hermaphroditism.Osmanthus fragrans L.has a... 详细信息

Several examples of androdioecy appear to have evolved from dioecy and have low male frequency(traits between males and hermaphrodites.The protandry in the same population and the protogyny in the same plant may promote the xenogamy between genders.The majority of flower traits related with the pollen production are different between males and hermaphrodites.Males bear more flowering nodes,and more flowers per node,and larger anther in all three populations.This characteristic demonstrated that males have more male advantage than hermaphrodites.Population genetic structure of O.fragrans is genetically homogeneous at the species level,and most variations exist within a population.The percentage of variation among populations(13%)and between males and hermaphrodites(0%)is low.Moreover,genetic differentiation was very low between genders not only among populations but also in the same population.This genetic variation could be attributed to the occurrence of high levels of xenogamy between genders.Therefore,high male frequency and more male fitness advantage in males are the essential conditions for this mating system,which plays an important role during population reproduction and regeneration.The 1:1 sex ratio could be the result of integrative effects of sexual system,mating system,and reproductive success.

关键词： traits ratio flowers

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The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon

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Horticulture Research 2023年第10期10卷 12-24页

作者： Guoli Li Lingli Tang Yuhua He Yongyang Xu Abdelhafid Bendahmane Jordi Garcia-Mas Tao Lin Guangwei Zhao National Key Laboratory for Germplasm Innovation&Utilization of Horticultural Crops Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenan 450009China China Agricultural University College of HorticultureBeijing 100193China National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanyaHainan 572024China Zhongyuan Research Center Chinese Academy of Agricultural SciencesXinxiang 453400China Institute of Plant Sciences Paris-Saclay(IPS2) INRAECNRSUniversity of Paris-SaclayUniversity of EvryUniversity of Paris-DiderotGif sur Yvette 91192France Centre for Research in Agricultural Genomics(CRAG)CSIC-IRTA-UAB-UB Edifici CRAGCampus UABBellaterra08193 BarcelonaSpain Institut de Recerca i Tecnologia Agroalimentàries(IRTA) Edifici CRAGCampus UABBellaterra08193 BarcelonaSpain

Melon(Cucumis melo L.)is an important vegetable crop that has an extensive history of cultivation.However,the genome of wild and semi-wild melon types that can be used for the analysis of agronomic traits is not yet available.Here we report a chromosome-level T2T genome assembly for 821(C.melo ssp.agrestis var.acidulus),a semi-wild melon with two haplotypes of∼373 Mb and∼364 Mb,respectively.Comparative genome analysis discovered a significant number of structural variants(SVs)between melo(C.melo ssp.melo)and agrestis(C.melo ssp.agrestis)genomes,including a copy number variation located in the ToLCNDV resistance locus on chromosome 11.Genome-wide association studies detected a significant signal associated with climacteric ripening and identified one candidate gene CM_ac12g14720.1(CmABA2),encoding a cytoplasmic short chain dehydrogenase/reductase,which controls the biosynthesis of abscisic acid.This study provides valuable genetic resources for future research on melon breeding.

关键词： agronomic traits structural

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Resequencing of sweetpotato germplasm resources reveals key loci associated with multiple agronomic traits

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Horticulture Research 2023年第1期10卷 128-139页

作者： Shizhuo Xiao Xibin Dai Lingxiao Zhao Zhilin Zhou Lukuan Zhao Pan Xu Bingqian Gao An Zhang Donglan Zhao Rui Yuan Yao Wang Jie Wang Qinglian Li Qinghe Cao Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute Chinese Agricultural Academy of SciencesXuzhou 221131China College of Pastoral Agriculture Science and Technology Lanzhou UniversityLanzhou 730020China

Sweetpotato is an important crop that exhibits hexaploidy and high heterozygosity,which limits gene mining for important agronomic traits.Here,314 sweetpotato germplasm resources were deeply resequenced,and 4599509 SNPs and 846654 InDels were generated,among which 196124 SNPs were nonsynonymous and 9690 InDels were frameshifted.Based on the Indels,genome-wide marker primers were designed,and 3219 of 40366 primer pairs were selected to construct the core InDel marker set.The molecular ID of 104 sweetpotato samples verified the availability of these primers.The sweetpotato population structures were then assessed through multiple approaches using SNPs,and diverse approaches demonstrated that population stratification was not obvious for most Chinese germplasm resources.As many as 20 important agronomic traits were evaluated,and a genome-wide association study was conducted on these traits.A total of 19 high-confidence loci were detected in both models.These loci included several candidate genes,such as IbMYB1,IbZEP1,and IbYABBY1,which might be involved in anthocyanin metabolism,carotenoid metabolism,and leaf morphogenesis,respectively.Among them,IbZEP1 and IbYABBY1 were first reported in sweetpotato.The variants in the promoter and the expression levels of IbZEP1 were significantly correlated with f lesh color(orange or not orange)in sweetpotato.The expression levels of IbYABBY1 were also correlated with leaf shape.These results will assist in genetic and breeding studies in sweetpotato.

关键词： germplasm breeding traits

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