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Characterization of QTL for unique agronomic traits of new-plant-type rice varieties using introgression lines of IR64

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The Crop Journal 2016年第1期4卷 12-20页

作者： Analiza G.Tagle Daisuke Fujita Leodegario A.Ebron Mary Jeanie Telebanco-Yanoria Kazuhiro Sasaki Tsutomu Ishimaru Yoshimichi Fukuta Nobuya Kobayashi International Rice Research Institute Japan International Research Center for Agricultural Sciences

To enhance the yield potential of an elite indica rice cultivar,an introgression(BC_3-derived) line of IR64,YTH288,was developed using a new-plant-type cultivar,IR66215-44-2-3,as a donor parent.YTH288 has agronomically valuable characteristics such as large panicles,few unproductive tillers,and large leaves inherited from NPT.To identify the genetic basis of these traits,we used 167 F_2 plants derived from a cross between IR64 and YTH288 to conduct QTL analysis for five agronomic traits:days to heading(DTH),culm length(CL),flag leaf length(FLL),flag leaf width(FLW),and filled spikelet number per panicle(FSN).Six putative QTL were detected:four on chromosome4(for CL,FLL,FLW,and FSN) and two on chromosome 2(for DTH and FLL).All QTL with the IR66215-44-2-3 allele,except that for FLL on chromosome 2,had positive effects on each trait.To confirm the effects of these putative QTL,we developed NILs with the IR64 genetic background by marker-assisted selection.We observed significant differences in several agronomic traits between IR64 and NILs that carried these QTL on chromosomes2 and 4.Additionally,four IR64-NILs carrying chromosomal segments derived from different NPT varieties on the long arm of chromosome 4 exhibited similar pleiotropic To enhance the yield potential of an elite indica rice cultivar, an introgression(BC3-derived) line of IR64, YTH288, was developed using a new-plant-type cultivar,IR66215-44-2-3, as a donor parent. YTH288 has agronomically valuable characteristics such as large panicles, few unproductive tillers, and large leaves inherited from NPT.To identify the genetic basis of these traits, we used 167 F2 plants derived from a cross between IR64 and YTH288 to conduct QTL analysis for five agronomic traits: days to heading(DTH), culm length(CL), flag leaf length(FLL), flag leaf width(FLW), and filled spikelet number per panicle(FSN). Six putative QTL were detected: four on chromosome4(for CL, FLL, FLW, and FSN) and two on chromosome 2(for DTH and FLL). All QTL with the IR66215-44-2-3 allele, exce

关键词： Agronomic traits Quantitative trait loci Near-isogenic lines New-plant-type rice variety Pleiotropic effect

Seasonal variations of leaf traits and drought adaptation strategies of four common woody species in South Texas, USA

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Journal of Forestry Research 2019年第5期30卷 1715-1725页

作者： Juan Qin Zhouping Shangguan Weimin Xi School of Resources and Environment Anhui Agricultural UniversityHefei 230036AnhuiChina Department of Biological and Health Sciences Texas A&M University-KingsvilleKingsvilleTX 78363USA State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau Northwest A&F UniversityYangling 712100ShaanxiChina

Understanding physiological responses and drought adaptation strategies of woody plant leaf traits in sub-humid to semi-arid regions is of vital importance to understand the interplay between ecological processes and plant resource-allocation strategies of different tree species.Seasonal variations of leaf morphological traits,stoichiometric traits and their relationships of two drought tolerant woody species,live oak(Quercus virginiana)and honey mesquite(Prosopis glandulosa)and two less drought tolerant species,sugarberry(Celtis laevigata)and white ash(Fraxinus americana)were analyzed in a sub-humid to semi-arid area of south Texas,USA.Our findings demonstrate that for the two drought tolerant species,the leguminous P.glandulosa had the highest specific leaf area,leaf N,P,and lowest leaf area and dry mass,indicating that P.glandulosa adapts to an arid habitat by decreasing leaf area,thus reducing water loss,reflecting a resource acquisition strategy.While the evergreen species Q.virginiana exhibited higher leaf dry mass,leaf dry matter content,C content,C:N,C:P and N:P ratios,adapts to an arid habitat through increased leaf thickness and thus reduced water loss,reflecting a resource conservation strategy in south Texas.For the two less drought tolerant deciduous species,the variations of leaf traits in C.laevigata and F.americana varied between Q.virginiana and P.glandulosa,reflecting a trade-off between rapid plant growth and nutrient maintenance in a semi-arid environment.

关键词： Drought adaptation strategies Leaf traits Seasonal variations South Texas Woody species

Identification of SNPs and expression patterns of FZD3 gene and its effect on wool traits in Chinese Merino sheep(Xinjiang Type)

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Journal of Integrative Agriculture 2019年第10期18卷 2351-2360页

作者： ZHAO Bing-ru FU Xue-feng TIAN Ke-chuan HUANG Xi-xia DI Jiang BAI Yan XU Xin-ming TIAN Yue-zhen WU Wei-wei ABLAT Sulayman ZENG Wei-dan HANIKEZI Tulafu College of Animal Science Xinjiang Agricultural UniversityUrumqi 830052P.R.China Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep Institute of Animal ScienceXinjiang Academy of Animal SciencesUrumqi 830011P.R.China

As a member of the Frizzled family, Frizzled3 (FZD3) is a receptor of the canonical Wnt signaling pathway and plays a vital role in mammalian hair follicle developmental processes. However, its effects on wool traits are not clear. The objectives of this study were to identify the single nucleotide polymorphisms (SNPs) and the expression patterns of FZD3 gene, and then to determine whether it affected wool traits of Chinese Merino sheep (Xinjiang Type) or not. PCR-single stranded conformational polymorphism (PCR-SSCP) and sequencing were used to identify mutation loci, and general linear model (GLM) with SAS 9.1 was used for the association analysis between wool traits and SNPs. Quantitative real-time PCR (qRT-PCR) was used to investigate FZD3 gene expression levels. The results showed that six exons of FZD3 gene were amplified and two mutation loci were identified in exon 1 (NC_019459.2: g.101771685 T>C (SNP1)) and exon 3 (NC_019459.2: g.101810848, A>C (SNP2)), respectively. Association analysis showed that SNP1 was significantly associated with mean fiber diameter (MFD)(P=0.04) and live weight (LW)(P=0.0004), SNP2 was significantly associated with greasy fleece weight (GFW)(P=0.04). The expression level of FZD3 gene in skin tissues of the superfine wool (SF) group was significantly lower (Ptraits and two identified SNPs might serve as potential and valuable genetic markers for sheep breeding and lay a molecular genetic foundation for sheep marker-assisted selection (MAS).

关键词： Chinese Merino sheep (Xinjiang Type) FZD3 single nucleotide polymorphism (SNP) expression pattern association analysis wool traits

Genetic diversity and association analyses of fruit traits with microsatellite ISSRs in Sapindus

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Journal of Forestry Research 2019年第1期30卷 193-203页

作者： Caowen Sun Liming Jia Benye Xi Jiming Liu Lianchun Wang Xuehuang Weng Ministry of Education Key Laboratory of Silviculture and Conservation Beijing Forestry University

Sapindus mukorossi Gaertn. and S. delavayi Franchet are among the most valuable species in the genus Sapindus for their commercially exploitable plant oils and chemicals. However, few studies have addressed genetic variation and improvement for either species. We evaluated the genetic diversity of germplasm from selected plus trees within a wide region and established the relationship between fruit traits and molecular markers. An association analysis based on inter-simple sequence repeats(ISSRs)provided a genetic basis for studies of fruit traits. A total of 247 loci were detected by scanning 61 trees of S. mukorossi and S. delavayi using 16 ISSR markers. Genetic diversity parameters were estimated for selected superior trees(or germplasm) and S. mukorossi and S. delavayi were categorized into two main groups, as well as into four groups within S. mukorossi. An association analysis between the ISSR markers and 14 fruit traits used the TASSEL MLM model. A genetic structure analysis differentiated S.mukorossi and S. delavayi. Eighteen ISSR loci associated with 13 fruit traits(P<0.005) were identified, with 13, 1,and 4 loci associated with seed oil production, fruit saponin production, and fruit quality, respectively. Using this information, a core collection was selected with adequate genetic diversity and good seed oil characters. Our results demonstrate the feasibility of effectively estimating fruit trait associations in Sapindus using ISSR markers, and the method is applicable and valuable for select germplasm conservation. The markers obtained in this study are potentially useful for molecular-assisted breeding of Sapindus spp.

关键词： Inter-simple sequence repeats Sapindus Fruit traits Association analysis Genetic diversity

Low soil temperature and drought stress conditions at flowering stage affect physiology and pollen traits of rice

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Journal of Integrative Agriculture 2019年第8期18卷 1859-1870页

作者： RAO Gang-shun Umair Ashraf KONG Lei-lei MO Zhao-wen XIAO Li-zhong ZHONG Ke-you Fahd Rasul TANG Xiang-ru Department of Crop Science and Technology College of Agriculture South China Agricultural University/Scientific Observing and Experimental Station of Crop Cultivation in South China Minist ry of Agriculture and Rural Affairs Guangzhou 510642 P.R.China Department of Agronomy University of Agriculture Faisalabad 38040 Pakistan

Low temperature and drought stress are the major constraints in rice productivity worldwide. This study investigated the influence of low soil temperature and/or drought stress on physiology and pollen traits of two rice genotypes viz., Guinongzhan and Yueza 763 at flowering stage. The experiment included four treatments, i.e., under the greenhouse natural growth conditions (UC) taken as control, drought stress (DS), the soil water potential was kept at ?0.035 to ?0.045 MPa (DS), low soil temperature (LT) maintained at 19 to 21℃, combined LT and DS (LT+DS, LD). Results showed that LT, DS, and LD substantially reduced net photosynthetic rate (Pn) and the maximal photochemical efficiency of PSII (Fv/Fm), whilst transpiration rate (Tr) was markedly enhanced by under LT in both rice genotypes. The malondialdehyde (MDA) contents were enhanced under LT, DS, and LD in Guinongzhan, whilst the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were regulated by LT, DS, and LD in both rice genotypes. Furthermore, anther dehiscence rate, pollen numbers on stigma, pollen viability and pollen germination rate, and anther starch contents were obviously reduced under LT and DS of both rice genotypes. Stress conditions substantially reduced the yield and yield components, i.e., effective panicles, seed set percentage, grain/panicles, 1000-grain weight, and grain yield of both genotypes and the effects were more apparent in Guinongzhan than those in Yueza 763 whilst combined LT and DS proved more damaging than individual stress.

关键词： antioxidant enzymes cold stress pollen traits photosynthesis rice yield

Genetic variations in plant architecture traits in cotton(Gossypium hirsutum) revealed by a genomewide association study

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The Crop Journal 2019年第2期7卷 209-216页

作者： Tianwang Wen Baosheng Dai Tao Wang Xinxin Liu Chunyuan You Zhongxu Lin National Key Laboratory of Crop Genetic Improvement College of Plant Science and Technology Huazhong Agricultural University Huanggang Academy of Agricultural Sciences Cotton Research Institute Shihezi Academy of Agriculture Science

Plant architecture traits influence crop yield. An understanding of the genetic basis of cotton plant architecture traits is beneficial for identifying favorable alleles and functional genes and breeding elite cultivars. We collected 121 cotton accessions including 100 brownfiber and 21 white-fiber accessions, genotyped them by whole-genome resequencing, and phenotyped them in multiple environments. This genome-wide association study(GWAS)identified 11 quantitative trait loci(QTL) for two plant architecture traits: plant height and fruit spur branch number. Negative-effect alleles were enriched in the elite cultivars. Based on these QTL, gene annotation information, and published QTL, candidate genes and natural genetic variations in four QTL were identified. Ghir_D02 G017510 and Ghir_D02 G017600 were identified as candidate genes for qD02-FSBN-1, and a premature start codon gain variation was found in Ghir_D02 G017510. Ghir_A12 G026570, the candidate gene of qA12-FSBN-2, belongs to the pectin lyase-like superfamily, and a significantly associated SNP, A12_105366045(T/C), in this gene represents an amino acid change. The QTL, candidate genes, and associated natural variations in this study are expected to lay a foundation for studying functional genes and developing breeding programs for desirable architecture in brown-fiber cotton.

关键词： Brown-fiber cotton Plant architecture traits GWAS QTL Genetic variation

Identification of QTL for kernel number-related traits in a rice chromosome segment substitution line and fine mapping of qSP1

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The Crop Journal 2019年第4期7卷 494-503页

作者： Fuying Ma Xiaoyan Zhu Hui Wang Shiming Wang Guoqing Cui Ting Zhang Zhenglin Yang Guanghua He Yinghua Ling Nan Wang Fangming Zhao Rice Research Institute Academy of Agricultural Sciences Southwest University

A chromosome segment substitution line (CSSL) is a powerful tool for combining quantitative trait locus (QTL) mapping with the pyramiding of desirable alleles. The rice CSSL Z1364 with increased kernel number was identified in a BC3F8 population derived from a cross of Nipponbare as the recipient with Xihui 18 as the donor parent. Z1364 carried three substitution segments distributed on chromosomes 1, 6, and 8. The mean substitution length was 1.19 Mb. Of 17 QTL identified on the substitution segments, qSP1 for spikelets per panicle, qSSD1 for seed-set density, and qNSB1 for number of secondary branches explained respectively 57.34%, 87.7%, and 49.44% of the corresponding phenotypic variance and were all linked to RM6777. Chi-square analysis showed that the increased kernel number in Z1364 was inherited recessively by a single gene. By fine mapping, qSP1 was delimited to a 50-kb region on the short arm of chromosome 1. Based on DNA sequence, a previously uncharacterized rice homolog of Arabidopsis thaliana AT4G32551 was identified as a candidate gene for qSP1 in which mutation increases the number of spikelets and kernels in Z1364. qSP1 was expressed in all tissues, but particularly in 1-cm panicles. The expression levels of OsMADS22, GN1A, and DST were upregulated and those of LAX2, GNP1, and GHD7 were downregulated in Nipponbare. These results provide a foundation for functional research on qSP1.

关键词： Rice Chromosome segment substitution line Increased number of kernels qSP1 QTL mapping for yield traits

Joint association analysis method to dissect complex genetic architecture of multiple genetically related traits

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The Crop Journal 2020年第5期8卷 733-744页

作者： Feng Lin Guoan Qi Ting Xu Xiangyang Lou Yongbo Hong Haiming Xu Institute of Crop Science College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058ZhejiangChina Department of Mathematics Zhejiang UniversityHangzhou 310058ZhejiangChina Department of Biostatistics Colleges of PHHP and the College of MedicineUniversity of FloridaGainesvilleFL 32610USA State Key Laboratory of Rice Biology and Zhejiang Key Laboratory of Super Rice Research China National Rice Research InstituteHangzhou 311401ZhejiangChina

Genome-wide association study(GWAS)has been a standard approach to discover the genetic determinants underlying complex traits.It is a major challenge in GWAS how to improve analysis power,uncover complex genetic correlation,and reveal gene-gene and gene-environment interactions through integrated analysis of multiple genetically related traits.To combat these challenges,we proposed a mixed linear model-based joint association analysis method for multiple traits,which include epistasis and geneenvironment interaction in the mapping model and utilize within-trait variance and between-trait covariance simultaneously;A F-statistics based on Wilks statistics is used to test the significance of each SNP and paired interacted SNPs,each genetic effects of QTS are estimated and tested by the MCMC method based on a QTS full model.Simulations showed that the multi-trait GWAS method could provide increased power in detecting pleiotropic loci affecting more than one trait,and can unbiasedly estimate effects of QTS.To demonstrate the performance of the proposed method,we analyzed four blood lipid traits in Multi-Ethnic Study of Atherosclerosis(MESA)Cohort and two yield-related traits in a rice immortalized F2 dataset.A software package was developed for the proposed method.

关键词： traits analysis complex

bHLH genes polymorphisms and their association with growth traits in the Pacifi c oyster Crassostrea gigas

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Journal of Oceanology and Limnology 2020年第3期38卷 862-868页

作者： CHEN Na LI Li LI Chenghua LIN Zhihua MENG Jie LIU Sheng SONG Kai BAO Yongbo Zhejiang Key Laboratory of Aquatic Germplasm Resources College of Biological&Environmental SciencesZhejiang Wanli UniversityNingbo 315121China School of Marine Sciences Ningbo UniversityNingbo 315211China Key Laboratory of Experimental Marine Biology Institute of OceanologyChinese Academy of SciencesQingdao 266071China

The basic helix-loop-helix(bHLH)genes encode a large superfamily of transcription factors in the Pacific oyster(Crassostrea gigas),and play a very important role in regulation of growth and development.To investigate the oyster growth traits and the associations with bHLH genes variations,we analyzed the gene polymorphisms-traits association in a wild population,and confirmed the results in another independent wild population by targeted gene re-sequencing and SNPshot analysis.After screening the single nucleotide polymorphisms(SNPs)in three candidate genes of the bHLH family(88 bHLH genes in two wild oyster populations in total),we identified the allele CgLoblHLH4-T/G located in the exon of the CgLoblHLH4 gene.This allele is a non-synonymous mutation(Phe/Leu)with an extremely significant association with shell width(Ptraits that could be used in breeding in C.gigas in the future.

关键词： Crassostrea gigas basic helix-loop-helix(bHLH) re-sequencing single nucleotide polymorphism(SNP)shot growth traits