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The Crop Journal 2024年第3期12卷 866-879页

作者： Haozhe Tan Binghui Tang Mengling Sun Qiulu Yin Yizan Ma Jianying Li Pengcheng Wang Zhonghua Li Guannan Zhao Maojun Wang Xianlong Zhang Chunyuan You Lili Tu National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070HubeiChina cotton research institute Shihezi Academy of Agriculture ScienceShihezi 832000XinjiangChina

cotton fiber is one of the main raw materials for the textile *** recent years,many cotton fiber quality QTL have been identified,but few were applied in *** this study,a genome wide association study(GWAS)of fiber-quality traits in 265 upland cotton breeding intermediate lines(GhBreeding),combined with genome-wide selective sweep analysis(GSSA)and genomic selection(GS),revealed 25 *** of these QTL were ignored by only using *** CRISPR/Cas9 mutants of GhMYB_D13 had shorter fiber,which indicates the credibility of QTL to a certain *** these QTL were verified in other cotton natural populations,5 stable QTL were found having broad potential for application in ***,among these 5 stable QTL,superior genotypes of 4 showed an enrichment in most improved new varieties widely cultivated *** findings provide insights for how to identify more QTL through combined multiple genomic analysis to apply in breeding.

关键词： cotton fiber quality breeding GWAS Genome-wide selective sweep analysis Genomic selection InDel markers

Identification of candidate genes for early-maturity traits by combining BSA-seq and QTL mapping in upland cotton(Gossypium hirsutum L.)

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Journal of Integrative agriculture 2024年第10期23卷 3472-3486页

作者： Liang Ma Tingli Hu Meng Kang Xiaokang Fu Pengyun Chen Fei Wei Hongliang Jian Xiaoyan Lü Meng Zhang Yonglin Yang State Key Laboratory of cotton Bio-breeding and Integrated Utilization/institute of cotton research Chinese Academy ofAgricultural SciencesAnyang 455000China School of agriculture Henan Institute of Science and TechnologyXinxiang 453003China shihezi academy of Agricultural sciences Shihezi 832099China

cotton breeding for the development of early-maturing varieties is an effective way to improve multiple cropping indexes and alleviate the conflict between grains and cotton in the cultivated fields in *** the present study,we aimed to identify upland cotton quantitative trait loci(QTLs)and candidate genes related to early-maturity traits,including whole growth period(WGP),flowering timing(FT),node of the first fruiting branch(NFFB),height of the node of the first fruiting branch(HNFFB),and plant height(PH).An early-maturing variety,CCRI50,and a latematuring variety,Guoxinmian 11,were crossed to obtain biparental *** populations were used to map QTLs for the early-maturity traits for two years(2020 and 2021).With BSA-seq analysis based on the data of population 2020,the candidate regions related to early maturity were found to be located on chromosome *** then developed 22 polymorphic insertions or deletions(InDel)markers to further narrow down the candidate regions,resulting in the detection of five and four QTLs in the 2020 and 2021 populations,*** to the results of QTL mapping,two candidate regions(InDel_G286-InDel_G144 and InDel_G24-InDel_G43)were *** these regions,three genes(GH_D03G0451,GH_D03G0649,and GH_D03G1180)have nonsynonymous mutations in their exons and one gene(GH_D03G0450)has SNP variations in the upstream sequence between CCRI50 and Guoxinmian *** four genes also showed dominant expression in the floral *** expression levels of GH_D03G0451,GH_D03G0649 and GH_D03G1180 were significantly higher in CCRI50 than in Guoxinmian 11 during the bud differentiation stages,while GH_D03G0450 showed the opposite *** functional verification of GH_D03G0451 indicated that the GH_D03G0451-silenced plants showed a delay in the flowering *** results suggest that these are the candidate genes for cotton early maturity,and they may be used for breeding early-maturity cotton varieties.

关键词： cotton genomics early-maturity traits BSA-seq QTL mapping molecular breeding

Straw return increases crop production by improving soil organic carbon sequestration and soil aggregation in a long-term wheat-cotton cropping system

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Journal of Integrative agriculture 2024年第2期23卷 669-679页

作者： Changqin Yang Xiaojing Wang Jianan Li Guowei Zhang Hongmei Shu Wei Hu Huanyong Han Ruixian Liu Zichun Guo institute of Industrial Crops Jiangsu Academy of Agricultural Sciences/Key Laboratory of Cotton and RapeseedMinistry of Agriculture and Rural AffairsNanjing 210014China College of Life sciences and Food Engineering Huaiyin Institute of TechnologyHuai’an 223003China College of agriculture Nanjing Agricultural UniversityNanjing 210095China cotton research institute Xinjiang Academy of Agricultural and Reclamation ScienceShihezi 832000China institute of Soil science Chinese Academy of Sciences/State Key Laboratory of Soil and Sustainable AgricultureNanjing 210008China

Straw return is a promising strategy for managing soil organic carbon(SOC)and improving yield ***,the optimal straw return strategy for sustainable crop production in the wheat(Triticum aestivum L.)-cotton(Gossypium hirsutum L.)cropping system remains *** objective of this study was to quantify the long-term(10 years)impact of carbon(C)input on SOC sequestration,soil aggregation and crop yields in a wheat-cotton cropping system in the Yangtze River Valley,*** treatments were arranged with a single-factor randomized design as follows:no straw return(Control),return of wheat straw only(Wt),return of cotton straw only(Ct),return of 50%wheat and 50%cotton straw(Wh-Ch)and return of 100%wheat and 100%cotton straw(Wt-Ct).In comparison to the Control,the SOC content increased by 8.4 to 20.2%under straw return.A significant linear positive correlation between SOC sequestration and C input(1.42-7.19 Mg ha^(−1)yr^(−1))(P2 and 1-2 mm at the 0-20 cm soil depth were also significantly elevated under straw return,with the greatest increase of the aggregate stability in the Wt-Ct treatment(28.1%).The average wheat yields increased by 12.4-36.0%and cotton yields increased by 29.4-73.7%,and significantly linear positive correlations were also detected between C input and the yields of wheat and *** average sustainable yield index(SYI)reached a maximum value of 0.69 when the C input was 7.08 Mg ha^(−1)yr^(−1),which was close to the maximum value(SYI of 0.69,C input of 7.19 Mg ha^(−1)yr^(-1))in the Wt-Ct ***,the return of both wheat and cotton straw was the best strategy for improving SOC sequestration,soil aggregation,yields and their sustainability in the wheat-cotton rotation system.

关键词： straw return crop yields SOC soil aggregates wheat-cotton cropping system

Identification of candidate genes for early-maturity traits by combining BSA-seq and QTL mapping in upland cotton(Gossypium hirsutum L.)

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Journal of Integrative agriculture 2024年第10期 3472-3486页

作者： Liang Ma Tingli Hu Meng Kang Xiaokang Fu Pengyun Chen Fei Wei Hongliang Jian Xiaoyan Lü Meng Zhang Yonglin Yang State Key Laboratory of cotton Bio-breeding and Integrated Utilization/institute of cotton research Chinese Academy of Agricultural Sciences School of agriculture Henan Institute of Science and Technology shihezi academy of Agricultural sciences

cotton breeding for the development of early-maturing varieties is an effective way to improve multiple cropping indexes and alleviate the conflict between grains and cotton in the cultivated fields in *** the present study,we aimed to identify upland cotton quantitative trait loci (QTLs) and candidate genes related to early-maturity traits,including whole growth period (WGP),flowering timing (FT),node of the first fruiting branch (NFFB),height of the node of the first fruiting branch (HNFFB),and plant height (PH).An early-maturing variety,CCRI50,and a latematuring variety,Guoxinmian 11,were crossed to obtain biparental *** populations were used to map QTLs for the early-maturity traits for two years (2020 and 2021).With BSA-seq analysis based on the data of population 2020,the candidate regions related to early maturity were found to be located on chromosome *** then developed 22 polymorphic insertions or deletions (InDel) markers to further narrow down the candidate regions,resulting in the detection of five and four QTLs in the 2020 and 2021 populations,*** to the results of QTL mapping,two candidate regions (InDel＿G286-InDel＿G144 and InDel＿G24-InDel＿G43)were *** these regions,three genes (GH＿D03G0451,GH＿D03G0649,and GH＿D03G1180) have nonsynonymous mutations in their exons and one gene (GH＿D03G0450) has SNP variations in the upstream sequence between CCRI50 and Guoxinmian *** four genes also showed dominant expression in the floral *** expression levels of GH＿D03G0451,GH＿D03G0649 and GH＿D03G1180 were significantly higher in CCRI50 than in Guoxinmian 11 during the bud differentiation stages,while GH＿D03G0450 showed the opposite *** functional verification of GH＿D03G0451 indicated that the GH＿D03G0451-silenced plants showed a delay in the flowering *** results suggest that these are the candidate genes for cotton early maturity,and they may be used for breeding early-maturity cotton varieti

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cotton ethylene response factor Gh ERF91 is involved in the defense against Verticillium dahliae

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Journal of Integrative agriculture 2024年第10期23卷 3328-3342页

作者： Nurimanguli Aini Yuanlong Wu Zhenyuan Pan Yizan Ma Qiushuang An Guangling Shui Panxia Shao Dingyi Yang Hairong Lin Binghui Tang Xin Wei Chunyuan You Longfu Zhu Dawei Zhang Zhongxu Lin Xinhui Nie Key Laboratory of Oasis Eco-agriculture Xinjiang Production and Construction Group/Agricultural CollegeShihezi UniversityShihezi 832003China National Key Laboratory of Crop Genetic Improvement/College of Plant sciences&Technology Huazhong AgriculturalUniversityWuhan 430070China cotton research institute Shihezi Academy of Agricultural ScienceShihezi 832011China institute of Economic Crops Xinjiang Academy of Agricultural SciencesUrumqi 830091China

Verticillium dahliae causes significant losses in cotton *** reveal the mechanism of the defense response to *** in cotton,transcriptomic analyses were performed using cotton cultivars M138(***-resistant)and P2(***-susceptible).The results revealed 11,076 and 6,640 differentially expressed genes(DEGs)in response to ***,*** weighted gene co-expression network analysis of 4,633 transcription factors(TFs)indicated a“MEblue”module containing 654 TFs that strongly correlate with resistance to *** these TFs,the ethylene response factor Ghi_A05G10166(GhERF91)was identified as a putative hub gene with a defense response against ***.A virus-induced gene silencing assay and exogenous application of ethephon showed that GhERF91 is activated by ethylene and positively regulates the response to *** exposure in *** study provides fundamental transcriptome data and a putative causal gene(GhERF91)associated with resistance to ***,as well as genetic resources for breeding ***-resistant cotton.

关键词： cotton Verticillium wilt RNA-sequencing GhERF91 virus-induced gene silencing

Biology of Hippo signaling pathway:Skeletal muscle development and beyond

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Journal of Integrative agriculture 2024年第6期23卷 1825-1838页

作者： Shuqi Qin Chaocheng Li Haiyan Lu Yulong Feng Tao Guo Yusong Han Yongsheng Zhang Zhonglin Tang Xinjiang Characteristic Livestock Breeding and Reproduction Team College of Animal Science and TechnologyShihezi UniversityShihezi 832003China Lanzhou Veterinary research institute Chinese Academy of Agricultural SciencesLanzhou 730046China Kunpeng institute of Modern agriculture at Foshan Foshan 528226China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China

Global demand for farm animals and their meat products i.e.,pork,chicken and other livestock meat,is steadily *** the ongoing life science research and the rapid development of biotechnology,it is a great opportunity to develop advanced molecular breeding markers to efficiently improve animal meat production *** is an important study subject because of its crucial role in the regulation of organ *** recent years,with the increase of research on Hippo signaling pathway,the integrative application of multi-omics technologies such as genomics,transcriptomics,proteomics,and metabolomics can help promote the in-depth involvement of Hippo signaling pathway in skeletal muscle development *** Hippo signaling pathway plays a key role in many biological events,including cell division,cell migration,cell proliferation,cell differentiation,cell apoptosis,as well as cell adhesion,cell polarity,homeostasis,maintenance of the face of mechanical overload,*** influence on the development of skeletal muscle has important research value for enhancing the efficiency of animal husbandry *** this study,we traced the origin of the Hippo pathway,comprehensively sorted out all the functional factors found in the pathway,deeply analyzed the molecular mechanism of its function,and classified it from a novel perspective based on its main functional domain and mode of *** aim is to systematically explore its regulatory role throughout skeletal muscle *** specifically focus on the Hippo signaling pathway in embryonic stem cell development,muscle satellite cell fate determination,myogenesis,skeletal muscle meat production and organ size regulation,muscle hypertrophy and atrophy,muscle fiber formation and its transformation between different types,and *** roles in proliferation and regeneration are methodically summarized and analyzed *** summary and prospect of the Hippo signaling pathway within this a

关键词： Hippo skeletal muscle organ size myogenesis C2C12 livestock animals

cotton ethylene response factor Gh ERF91 is involved in the defense against Verticillium dahliae

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Journal of Integrative agriculture 2024年第10期 3328-3342页

作者： Nurimanguli Aini Yuanlong Wu Zhenyuan Pan Yizan Ma Qiushuang An Guangling Shui Panxia Shao Dingyi Yang Hairong Lin Binghui Tang Xin Wei Chunyuan You Longfu Zhu Dawei Zhang Zhongxu Lin Xinhui Nie Key Laboratory of Oasis Eco-agriculture Xinjiang Production and Construction Group/Agricultural College Shihezi University National Key Laboratory of Crop Genetic Improvement/College of Plant sciences & Technology Huazhong Agricultural University cotton research institute Shihezi Academy of Agricultural Science institute of Economic Crops Xinjiang Academy of Agricultural Sciences

Verticillium dahliae causes significant losses in cotton production. To reveal the mechanism of the defense response to V. dahliae in cotton, transcriptomic analyses were performed using cotton cultivars M138(V. dahliae-resistant)and P2(V. dahliae-susceptible). The results revealed 11,076 and 6,640 differentially expressed genes(DEGs)in response to V. dahliae, respectively. The weighted gene co-expression network analysis of 4,633 transcription factors(TFs) indicated a “MEblue” module containing 654 TFs that strongly correlate with resistance to V. *** these TFs, the ethylene response factor Ghi＿A05G10166(GhERF91) was identified as a putative hub gene with a defense response against V. dahliae. A virus-induced gene silencing assay and exogenous application of ethephon showed that GhERF91 is activated by ethylene and positively regulates the response to V. dahliae exposure in cotton. This study provides fundamental transcriptome data and a putative causal gene(GhERF91)associated with resistance to V. dahliae, as well as genetic resources for breeding V. dahliae-resistant cotton.

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Identification of S-RNase genotype and analysis of its origin and evolutionary patterns in Malus plants

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Journal of Integrative agriculture 2024年第4期23卷 1205-1221页

作者： Zhao Liu Yuan Gao Kun Wang Jianrong Feng Simiao Sun Xiang Lu Lin Wang Wen Tian Guangyi Wang Zichen Li Qingshan Li Lianwen Li Dajiang Wang research institute of Pomology Chinese Academy of Agricultural Sciences/Key Laboratory of Horticultural Crops Germplasm Resources UtilizationMinistry of Agriculture and Rural AffairsXingcheng 125100China College of agriculture Shihezi University/Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction CorpsShihezi 832000China

Identification of the S genotype of Malus plants will greatly promote the discovery of new genes,the cultivation and production of apple,the breeding of new varieties,and the origin and evolution of self-incompatibility in Malus *** this experiment,88 Malus germplasm resources,such as Aihuahong,Xishuhaitang,and Reguanzi,were used as *** gene-specific primer combinations were used in the genotype *** amplification using leaf DNA produced a single S-RNase gene fragment in all *** results revealed that 70 of the identified materials obtained a complete S-RNase genotype,while only one S-RNase gene was found in 18 of *** homology comparison and analysis,13 S-RNase genotypes were obtained:S_(1)S_(2)(Aihuahong,etc.),S_(1)S_(28)(Xixian Haitang,etc.),S_(1)S_(51)(Hebei Pingdinghaitang),S_(1)S_(3)(Xiangyangcun Daguo,etc.),S_(2)S_(3)(Zhaiyehaitang,etc.),S_(3)S_(51)(Xishan 1),S_(3)S_(28)(Huangselihaerde,etc.),S_(2)S_(28)(Honghaitang,etc.),S_(4)S_(28)(Bo 11),S_(7)S_(28)(Jiuquan Shaguo),S_(10)S_e(Dongchengguan 13),S_(10)S_(21)(Dongxiangjiao)and S_(3)S_(51)(Xiongyue Haitang).Simultaneously,the frequency of the S gene in the tested materials was *** findings revealed that different S genes had varying frequencies in Malus resources,as well as varying frequencies between intraspecific and interspecific.S_(3) had the highest frequency of 68.18%,followed by S_(1)(42.04%).In addition,the phylogenetic tree and origin evolution analysis revealed that the S gene differentiation was completed prior to the formation of various apple species,that cultivated species also evolved new S genes,and that the S_(50) gene is the oldest S allele in Malus *** S_(1),S_(29),and S_(33) genes in apple-cultivated species,on the other hand,may have originated in ***,***,and ***,*** addition to ***,*** and *** may have also played a role in the origin and evolution of some Chine

关键词： Malus S-RNase genotype self-incompatibility origin and evolution

Identification of SSR markers linked to the abscission of cotton boll traits and mining germplasm in cotton

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Journal of cotton research 2024年第2期7卷 177-187页

作者： SHUI Guangling LIN Hairong MA Xiaomei ZHU Bo HAN Peng AINI Nurimanguli GUO Chunping WU Yuanlong PAN Zhenyuan YOU Chunyuan SONG Guoli NIE Xinhui Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan Agricultural CollegeShihezi UniversityShiheziXinjiang 832003China cotton institute Xinjiang Academy of Agriculture and Reclamation ScienceShiheziXinjiang 832000China Agricultural science research institute of the 5th Division of Xinjiang Production and Construction Corps ShuangheXinjiang 833408China Modern Agricultural College Kashi UniversityKashiXinjiang 844000China National Key Laboratory of Crop Genetic Improvement College of Plant Sciences&TechnologyHuazhong Agricultural UniversityWuhanHubei 430070China National Key Laboratory of cotton Bio‑Breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenan 455000China

Background cotton is an economically important *** is crucial to find an effective method to improve cotton yield,and one approach is to decrease the abscission of cotton bolls and ***,the lack of knowledge of the genetic and molecular mechanisms underlying cotton boll abscission traits has hindered genetic *** Pearson’s correlation analysis revealed a significant positive correlation between boll abscission rates 1(AR1)and boll abscission rates 2(AR2).A genome-wide association study was conducted on 145 loci that exhibited high polymorphism and were uniformly distributed across 26 chromosomes(pair).The study revealed 18,46,and 62 markers that were significantly associated with boll abscission,fiber quality,and yield traits(Pcotton boll abscission trait,whereas MON_CGR5732a was associated with cotton boll abscission and fiber quality *** of the marker loci identified in this study had been previously *** on phenotypic effects,six typical cultivars with elite alleles related to cotton boll abscission,fiber quality,and yield traits were *** cultivars hold great promise for widespread utilization in breeding *** These results lay the foundation for understanding the molecular regulatory mechanism of cotton boll abscission and provide data for the future improvement of cotton breeding.

关键词： SSR Genome wide association studies Abscission Favorable alleles cotton Genetic improvement

Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice

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National science Review 2024年第4期11卷 55-69页

作者： Hua Wei Xianmeng Wang Zhipeng Zhang Longbo Yang Qianqian Zhang Yilin Li Huiying He Dandan Chen Bin Zhang Chongke Zheng Yue Leng Xinglan Cao Yan Cui Chuanlin Shi Yifan Liu Yang Lv Jie Ma Wenchuang He Xiangpei Liu Qiang Xu Qiaoling Yuan Xiaoman Yu Tianyi Wang Hongge Qian Xiaoxia Li Bintao Zhang Hong Zhang Wu Chen Mingliang Guo Xiaofan Dai Yuexing Wang Xiaoming Zheng Longbiao Guo Xianzhi Xie Qian Qian Lianguang Shang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences institute of Wetland agriculture and Ecology Shandong Academy of Agricultural Sciences State Key Laboratory of Rice Biology China National Rice Research Institute National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Science Chinese Academy of Agricultural Sciences Yazhouwan National Laboratory

For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610expression quantitative trait loci associated with the expression of 7787 and 9361 e Genes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5—a major salt-tolerant locus known as q STS5. Intriguingly, STG5 is required for maintaining Na+/K+homeostasis by directly regulating the transcription of multiple members of the Os HKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.

关键词： super pan-genome expression quantitative trait loci GWAS salt tolerance rice