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qtl analysis of early flowering of female flowers in zucchini(Cucurbita pepo L.)

Journal of Integrative Agriculture 2023年第11期22卷 3321-3330页

作者： QU Shu-ping YANG Dan YU Hai-yang CHEN Fang-yuan WANG Ke-xin DING Wen-qi XU Wen-long WANG Yun-li Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(Northeast Region) Ministry of Agriculture and Rural Affairs/College of Horticulture and Landscape ArchitectureNortheast Agricultural UniversityHarbin 150030P.R.China Laboratory of Molecular Breeding of Pumpkin College of Horticulture and Landscape ArchitectureNortheast Agricultural UniversityHarbin 150030P.R.China

Early flowering promotes early maturity, production, and the capacity to counteract biotic and abiotic stresses, making it an important agronomic trait in zucchini. The present study demonstrated that the zucchini inbred line ‘19’ consistently flowered early, taking significantly fewer days to bloom the first female flower(DFF) than the inbred line ‘113’. Genetic analysis revealed that DFF, an inheritable quantitative trait, is controlled by multiple genes. Based on the strategy of quantitative trait locus(qtl) sequencing(qtl-seq) combined with linkage analysis, three qtls for DFF were identified on chromosomes 4, 11, and 20. This study used additional F2 populations grown under different environmental conditions for qtl mapping analysis of DFF with insertion/deletion(InDel) markers to validate these results. Using the composite interval mapping(CIM) method of R/qtl software, we only identified one major locus under all environmental conditions, located in a 117-kb candidate region on chromosome 20. Based on gene annotation, gene sequence alignment, and qRT-PCR analysis, we found that the Cp4.1LG20g08050 gene encoding a RING finger protein may be a candidate gene for the opposite regulation of early flowering in zucchini. In summary, these results lay a foundation for a better understanding of early flowering and improving early flowering-based breeding strategies in zucchini.

关键词： Cucurbita pepo L. early flowering days to bloom the first female flower qtl analysis

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analysis of qtl for Seed Dormancy and Their Response to Dry Heat Treatment in Rice (Oryza sativa L.)

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Agricultural Sciences in China 2004年第9期3卷 641-648页

作者： TANGJiu-you JIANGLing ZHANGWen-wei WANGChun-ming LIUShi-jia CHENLiang-ming ZHAIHu-qu AtsushiYoshimura WANJian-min StateKeyLaboratoryofCropGeneticsandGermplasmEnhancement ResearchCenterofJiangsuPlantGeneEngineeringNanjingAgriculturalUniversityNanjing210095P.R.China ChineseAcademyofAgriculturalSciences Beijing100081P.R.China FacultyofAgriculture KyushuUniversityFukuoka812-8581Japan

Quantitative trait loci (qtl) controlling seed dormancy in rice were identified usingrecombinant inbred lines (RILs) population derived from the cross between a japonicavariety Kinmaze and an indica variety DV85. Seeds of two parental cultivars and each RILwere harvested in 35d after heading. The germination percentage of these seeds at 30℃for 7 days were measured as the degree of seed dormancy. qtl analysis was performed withWindows qtl Cartographer 1.13a program by composite interval mapping. A total of four qtlfor seed dormancy were detected on chromosome 2 (two regions), 5 and 11, respectively.Phenotypic variation explained by each qtl ranged from 8.37 to 17.40%. Responses of suchloci to a dormancy-breaking treatment with dry heat were further detected. The resultsshowed that two alleles of qDOR-2-1 and qDOR-5 from DV85 as well as the allele of qDOR-11 from Kinmaze increased the seed dormancy, which seemed to be easily broken by dry heattreatment. Such loci of seed dormancy may be applied to rice genetic improvement. Theallele of qDOR-2-2 from DV85 increased the seed dormancy, which could not be broken bydry heat treatment.

关键词： Rice(Oryza sativa L.) Seed dormancy RI population qtl analysis Dormancy- breaking by dry heat treatment

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Genetic analysis of leaffolder resistance in rice

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Journal of Genetics and Genomics 2010年第5期37卷 325-331页

作者： Yuchun Rao Guojun Dong Dali Zeng Jiang Hu Longjun Zeng Zhengyu Gao Guanghen Zhang Longbiao Guo Qian Qian State Key Laboratory of Rice Biology China National Rice Research Institute Hangzhou 310006 China Graduate School of Chinese Academy of Agriculture Science Beijing 100081 China

A double haploid （DH） population, which consists of 120 lines derived from anther culture of a typical indica and japonica hybrid ‘CJ06＇/‘TNI＇, was used to investigate the genetic basis for rice leaffolder resistance. Using a constructed molecular linkage map, five qtls for rolled leaves were detected on chromosomes 1, 2, 3, 4, and 8. The positive alleles from C J06 on chromosomes 3, 4, and 8 increased the resistance to rice leaffolder, and the alleles from TN1 on chromosomes 1 and 2 also enhanced resistance to leaffolder. The interactions between qtls were identified and tested, and four conditional interactions were acquired for resistance to rice leaffolder. These loci were located on chromosomes 2, 9, 10, and 11, respectively. qtl pyramiding indicated that the positive alleles affect resistance to leaffolder. The prospective application of this data in rice breeding was also discussed.

关键词： rice （Oryza sativa L.） rice leaffolder qtl analysis conditional interaction

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Identification of qtls Conferring Agronomic and Quality Traits in Hexaploid Wheat

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Journal of Integrative Agriculture 2012年第9期11卷 1399-1408页

作者： MAJun CSIRO Plant Industry St Lucia QLD 4067 Australia Key Laboratory for Crop Germplasm Resources of Hebei Province~College of Life Science Agricultural University of Hebei Baoding 071001 P.R.China School of Plant Biology The University of Western Australia Perth WA 6009 Australia

The availability of elite germplasm resources with high yield and quality potentials is very important for development of cultivars in wheat. Thus, seeking such resources has been the continuous effort of breeder community. In this study, genetic analysis of a novel resource, Triticum spelta line CSCR6, from Australia was made by use of a recombination inbred line （RIL） population of 82 individuals from the cross between CSCR6 and another Australian hexaploid wheat cultivar, Lang. Data of a multiple environmental test was employed to genetically dissect quantitative trait loci （qtl） for agronomic traits such as plant height （PH）, spike length （SL）, spikelet per spike （SPI）, grain number per spike （GNS） and thousand grains weight （TGW） and for quality traits including grain protein content （GPC）, gluten content （GC）, grain hardness （GH）, falling number （FN） and sedimentation value （SV）. A 24 qtls with additive effects were detected for all the investigated traits, and were located on chromosomes 1B, 1D, 2B, 3A, 3B, 3D, 4B, 5A, 5B, 7A, and 7B, respectively. Some qtls located on 2B and 4B showed higher explanation of phenotypic variances and were not obviously interacted with environment. A qtl in the marker interval of wPT-5334-wPT-4918 （near the locus barc 0199） on 4B gave the highest contribution ratio of 30.76% on PH, while Qgpc-4B and Qgc-4B gave 13.07 and 14.70% contribution ratio on GPC and GC, respectively. Qph-2B, Qgns-2B, and Qgpc-2B showed 13.36, 10.00, and 10.79% contribution ratio on PH, GNS and GPC, respectively. Also, a qtl on 5A, Qsl- 5A, could explain 25.12% of phenotypic variance on SL. For most of agronomic and quality traits, CSCR6 alleles produced increase effects. The fact that a number of loci affecting the investigated traits were detected in T. spelta line CSCR6 revealed that it could offer a new opportunity for the manipulation of these traits in wheat breeding programs.

关键词： wheat qtl analysis RILs agronomic traits quality traits

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qtl Mapping for Adult Plant Resistance to Powdery Mildew in Italian Wheat cv. Strampelli

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Journal of Integrative Agriculture 2013年第5期12卷 756-764页

作者： Asad Muhammad Azeem BAI Bin LAN Cai-xia YAN Jun XIA Xian-chun ZHANG Yong HE Zhong-hu National Wheat Improvement Center/National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural Sciences(CAAS) Cotton Research Institute Chinese Academy of Agricultural Sciences(CAAS) International Maize and Wheat Improvement Center(CIMMYT) China Office

The Italian wheat cv. Strampelli displays high resistance to powdery mildew caused by Blumeria graminis f. sp. tritici. The objective of this study was to map quantitative trait loci （qtls） for resistance to powdery mildew in a population of 249 F2：3 lines from Strampelli/Huixianhong. Adult plant powdery mildew tests were conducted over 2 yr in Beijing and 1 yr in Anyang and simple sequence repeat （SSR） markers were used for genotyping. qtls Qpm.caas-3BS, Qpm.eaas-5BL. 1, and Qpm.caas-7DS were consistent across environments whereas, Qpm.caas-2BS. 1 found in two environments, explained 0.4-1.6, 5.5-6.9, 27.1-34.5, and 1.0-3.5% of the phenotypic variation respectively. Qpm.caas-7DS corresponded to the genomic location of Pm38/Lr34/Yr18. Qpm.caas-4BL was identified in Anyang 2010 and Beijing 2011, accounting for 1.9-3.5% of phenotypic variation. Qpm.caas-2BS. 1 and Qpm.caas-5BL. 1 contributed by Strampelli and Qpm.caas-3BS by Huixianhong, seem to be new qtl for powdery mildew resistance. Qpm.caas-4BL, Qpm.caas-5BL.3, and Qpm.caas-7DS contributed by Strampelli appeared to be in the same genomic regions as those mapped previously for stripe rust resistance in the same population, indicating that these loci conferred resistance to both stripe rust and powdery mildew. Strampelli could be a valuable genetic resource for improving durable resistance to both powdery mildew and stripe rust in wheat.

关键词： qtl analysis SSR markers Blumeria graminis durable resistance Triticum aestivum L.

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qtl mapping of seedling biomass and root traits under different nitrogen conditions in bread wheat(Triticum aestivum L.)

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Journal of Integrative Agriculture 2021年第5期20卷 1180-1192页

作者： YANG Meng-jiao WANG Cai-rong Muhammad Adeel HASSAN WU Yu-ying XIA Xian-chun SHI Shu-bing XIAO Yong-gui HE Zhong-hu College of Agriculture Xinjiang Agricultural UniversityUrumqi 830052P.R.China National Wheat Improvement Centre Institute of Crop SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100081P.R.China Institute of Agricultural Science of Yili Prefecture Yining 835000P.R.China International Maize and Wheat Improvement Centre(CIMMYT)China Office c/o CAASBeijing 100081P.R.China

Plant nitrogen assimilation and use efficiency in the seedling's root system are beneficial for adult plants in field condition for yield enhancement.Identification of the genetic basis between root traits and N uptake plays a crucial role in wheat breeding.In the present study,198 doubled haploid lines from the cross of Yangmai 16/Zhongmai 895 were used to identify quantitative trait loci(qtls)underpinning four seedling biomass traits and five root system architecture(RSA)related traits.The plants were grown under hydroponic conditions with control,low and high N treatments(Ca(NO_(3))_(2)·4H_(2)O at 0,0.05 and 2.0 mmol L^(-1),respectively).Significant variations among the treatments and genotypes,and positive correlations between seedling biomass and RSA traits(r=0.20 to 0.98)were observed.Inclusive composite interval mapping based on a high-density map from the Wheat 660 K single nucleotide polymorphisms(SNP)array identified 51 qtls from the three N treatments.Twelve new qtls detected on chromosomes 1 AL(1)in the control,1 DS(2)in high N treatment,4 BL(5)in low and high N treatments,and 7 DS(3)and 7 DL(1)in low N treatments,are first reported in influencing the root and biomass related traits for N uptake.The most stable qtls(RRS.caas-4 DS)on chromosome 4 DS,which were related to ratio of root to shoot dry weight trait,was in close proximity of the Rht-D1 gene,and it showed high phenotypic effects,explaining 13.1%of the phenotypic variance.Twenty-eight qtls were clustered in 12 genetic regions.SNP markers tightly linked to two important qtls clusters C10 and C11 on chromosomes 6 BL and 7 BL were converted to kompetitive allele-specific PCR(KASP)assays that underpin important traits in root development,including root dry weight,root surface area and shoot dry weight.These qtls,clusters and KASP assays can greatly improve the efficiency of selection for root traits in wheat breeding programmes.

关键词： KASP marker qtl analysis root traits SNP array Triticum aestivum

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Construction of high-density SNP genetic maps and qtl mapping for dwarf-related traits in Litchi chinensis Sonn

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Journal of Integrative Agriculture 2021年第11期20卷 2900-2913页

作者： HU Fu-chu CHEN Zhe WANG Xiang-he WANG Jia-bao FAN Hong-yan QIN Yong-hua ZHAO Jie-tang HU Gui-bing State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(South China) Ministry of Agriculture and Rural Affairs/College of HorticultureSouth China Agricultural UniversityGuangzhou 510642P.R.China Key Laboratory of Tropical Fruit Tree Biology of Hainan Province/Institute of Tropical Fruit Trees Hainan Academy of Agricultural ScienceHaikou 571100P.R.China Environment and Plant Protection Institute Chinese Academy of Tropical Agricultural SciencesHaikou 571101P.R.China

Litchi chinensis Sonn is widely cultivated in subtropical regions and has an important economic value.A high-density genetic map is a valuable tool for mapping quantitative trait loci(qtl)and marker-assisted breeding programs.In this study,a single nucleotide polymorphism(SNP)-based high-density linkage map was constructed by a genotyping-by-sequencing(GBS)protocol using an F1 population of 178 progenies between two commercial litchi cultivars,‘Ziniangxi’(dwarf)and‘Feizixiao’(vigorous).The genetic map consisted of 3027 SNP markers with a total length of 1711.97 cM in 15 linkage groups(LGs)and an average marker distance of 0.57 cM.Based on this high-density linkage map and three years of phenotyping,a total of 37 qtls were detected for eight dwarf-related traits,including length of new branch(LNB),diameter of new branch(DNB),length of common petiole(LCP),diameter of common petiole(DCP),length of internode(LI),length of single leaf(LSL),width of single leaf(WSL),and plant height(PH).These qtls could explain 8.0 to 14.7%(mean=9.7%)of the phenotypic variation.Among them,several qtl clusters were observed,particularly on LG04 and LG11,which might show enrichment for genes regulating the dwarf-related traits in litchi.There were 126 candidate genes identified within the qtl regions,55 of which are differentially expressed genes by RNA-seq analysis between‘Ziniangxi’and‘Feizixiao’.These DEGs were found to participate in the regulation of cell development,material transportation,signal transduction,and plant morphogenesis,so they might play important roles in regulating plant dwarf-related traits.The high-density genetic map and qtls identification related to dwarf traits can provide a valuable genetic resource and a basis for marker-assisted selection and genomic studies of litchi.

关键词： Litchi chinensis SNP genetic map dwarf-related traits qtl analysis genotyping-by-sequencing(GBS)

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Identification of Quantitative Trait Locus for Overwintering Germinability in Rice(Oryza sativa L.)

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Journal of Integrative Agriculture 2012年第11期11卷 1767-1774页

作者： ZHAO Zheng-wu LUO An-cai LE Tao LI Shi-gui School of Life Sciences Chongqing Normal University Chongqing 400047 P.R.China Rice Research Institute Sichuan Agricultural University Chengdu 611130 P.R.China

312 recombinant inbred lines （RILs） in F9 from a cross between a overwintering cold-tolerant germplasm resource Glutinous rice 89-1（Gr 89-1） and a cold-sensitive variety Shuhui 527 was used for quantitative trait locus （qtl） analysis. The scores of percent ratooning germinability （PRG） and overwintering germinability （POG） were evaluated. The overwintering germination rate of axillary buds was scored to represent the overwintering germinability. Two significant qtls （qPRG-4 and qPRG-7） on chromosomes 4 and 7 were detected and explained 8.3 and 7.2% of the total phenotypic variation, respectively. Three significant qtls （qPOG-2, qPOG-3 and qPOG-7） were identified and mapped on chromosomes 2, 3, and 7, respectively. These qtls contributed 9.6, 6.7, and 17.8% of phenotypic variations, respectively. A comparative analysis using SSR markers closely linked to the three qtls for the overwintering revealed cold-tolerant individuals, which harbour the Glutinous rice 89-1 alleles at RM7110, RM250, RM418, and RM232, had a high percent overwintering germinability, while cold-sensitive individuals, which carry Shuhui 527 alleles at these loci, had a low percent overwintering germinability in the F2 population of Shuhui 527/Glutinous rice 89-1. This study demonstrated the utility of these SSR markers for selection of overwintering germinability genotypes.

关键词： rice （Oryza sativa L.） percent overwintering germlnability recombinant inbred lines qtl analysis coldtolerance

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analysis of qtls for the Trichome Density on the Upper and Downer Surface of Leaf Blade in Soybean [Glycine max (L.) Merr.]

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Agricultural Sciences in China 2009年第5期8卷 529-537页

作者： DU Wei-jun YU De-yue FU San-xiong National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement/Nanjing Agricultural University Nanjing 210095 P.R. China College of Agronomy Shanxi Agricultural University Taigu 030801 P.R.China

Trichomes （plant hairs） are present on nearly all land plants and are known to play important roles in plant protection, specifically against insect herbivory, drought, and UV radiation. The identification of quantitative trait loci （qtl） associated with trichome density should help to interpret the molecular genetic mechanism of soybean trichome density. 184 recombinant inbred lines （RILs）, derived from a cross between soybean cultivars Kefeng 1 and Nannong 1138-2 were used as segregating population for evaluation of TDU （trichome density on the upper surface of leaf blade） and TDD （trichome density on the downer surface of leaf blade）. A total of 15 qtl were detected on molecular linkage groups （MLG） A2, Dla, Dlb, E and H by composite interval mapping （CIM） and among all the qtl, qtuA2-1, qtuD 1 a-1, qtuD lb-2, qtuH-2 qtuE-1, qtdDlb-2, and qtdH- 2 were affirmed by multiple interval mapping （MIM）. The contribution ofphenotypic variance of qtuH-2 was 31.81 and 29.4% by CIM and MIM, respectively, suggesting it might be major gene Ps loci. Only 10 pairs of main qtl interactions for TDU were detected, explained a range of 0.2-5.1% of phenotypic variations for each pair for a total of 22.8%. The qtl on MLG Dlb affecting trichome density were mapped near to Rsc-7 conditioning resistance to SMV （soybean mosaic virus）. This study showed that the genetic mechanism of trichome density was the mixed major gene and polygene inheritance, and also suggested that the causal nature between trichome density and other agronomic traits.

关键词： soybean [Glycine max （L.） Merr.] TDU TDD RI Ls qtl analysis

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Coherent estimates of genetic effects with missing information

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Open Journal of Genetics 2012年第1期2卷 31-38页

作者： Carl Nettelblad Orjan Carlborg Ania Pino-Querido Jose M.Alvarez-Castro Department of Information Technology Uppsala UniversityUppsalaSweden Linnaeus Centre for Bioinformatics Uppsala UniversityUppsalaSweden Department of Animal Breeding and Genetics Swedish University of Agricultural SciencesUppsalaSweden Department of Genetics University of Santiago de CompostelaLugoSpain

Genetic effect estimates for loci detected in quantitative trait locus (qtl) mapping experiments depend upon two factors. First, they are parameterizations of the genotypic values determined by the model of genetic effects. Second, they are consequently also affected by the regression method used to estimate the genotypic values from the observed marker genotypes and phenotypes. There are two common causes for marker-genotype data to be incomplete in those experiments—missing marker-genotypes and within-interval mapping. Different regression methods tend to differ in how this missing information is represented and handled. In this communication we explain why the estimates of genetic effects of qtl obtained using standard regression methods are not coherent with the model of genetic effects and indeed show intrinsic inconsistencies when there is incomeplete genotype information. We then describe the interval mapping by imputations (IMI) regression method and prove that it overcomes those problems. A numerical example is used to illustrate the use of IMI and the consequences of using current methods of choice. IMI enables researchers to obtain estimates of genetic effects that are coherent with the model of genetic effects used, despite incomplete genotype information. Furthermore, because IMI allows orthogonal estimation of genetic effects, it shows potential performance advantages for being implemented in qtl mapping tools.

关键词： Genetic Effects Missing Genotypes Orthogonal Estimation qtl analysis

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