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Validation of qGSIO, a quantitative trait locus for grain size on the long arm of chromosome 10 in rice (Oryza sativa L.)

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Journal of Integrative Agriculture 2017年第1期16卷 16-26页

作者： WANG Zhen CHEN Jun-yu ZHU Yu-jun FAN Ye-yang ZHUANG Jie-yun State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement China National Rice Research Institute Hangzhou 310006 P.R. China

Grain size is a major determinant of grain weight and a trait having important impact on grain quality in rice. The objective of this study is to detect QTLs for grain size in rice and identify important QTLs that have not been well characterized before. The QTL mapping was first performed using three recombinant inbred line populations derived from indica rice crosses Teqing/IRBB lines, Zhenshan 97/Milyang 46, Xieqingzao/Milyang 46. Fourteen QTLs for grain length and 10 QTLs for grain width were detected, including seven shared by two populations and 17 found in one population. Three of the seven com- mon QTLs were found to coincide in position with those that have been cloned and the four others remained to be clarified. One of them, qGSIO located in the interval RM6100-RM228 on the long arm of chromosome 10, was validated using F2：3 populations and near isogenic lines derived from residual heterozygotes for the interval RM6100-RM228. The QTL was found to have a considerable effect on grain size and grain weight, and a small effect on grain number. This region was also previously detected for quality traits in rice in a number of studies, providing a good candidate for functional analysis and breeding utilization.

关键词： grain size quantitative trait locus residual heterozygote rice (Oryza sativa L.)

Mapping of qTGW1.1,a quantitative trait locus for 1000-Grain Weight in Rice (Oryza sativa L.)

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Rice science 2015年第1期22卷 9-15页

作者： ZHANG Hong-wei CHEN Yu-yu CHEN Jun-yu ZHU Yu-jun HUANG De-run FAN Ye-yang ZHUANG Jie-yun State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement China National Rice Research Institute

1000-grain weight （ TGW） is one ot the three component traits ot the grain yiela in rice （Oryza sativa L）. This study was conducted to validate and fine-map qTGWl. 1, a minor QTL for TGW which was previously located in a 3.7-Mb region on the long arm of rice chromosome 1. Five sets of near isogenic lines （NILs） were developed from two BC2F4 populations of the indica rice cross Zhenshan 973/Milyang 46 The NIL sets consisted of two homozygous genotypic groups differing in the regions RM11448-RM11522, RM11448-RM11549, RM1232-RM11615, RM11543-RM11554 and RM11569-RM11621, respectively. Four traits, including TGW, grain length, grain width and heading date, were measured. Phenotypic difference between the two genotypic groups in each NIL population was analyzed using SAS procedure GLM. Significant QTL effects were detected on TGW with the Zhenshan 97 allele increasing grain weight by 0.12 g to 0.14 g and explaining 8.30% to 15.19% of the phenotypic variance. Significant effects were also observed for grain length and width, whereas no significant effect was found for heading date. Based on comparison among the five NILs on the segregating regions and the results of QTL analysis, qTGWl. 1 was delimited to a 376.9-kb region flanked by DNA markers Wn28382 and RMl1554. Our results indicate that the effects of minor QTLs could be steadily detected in a highly isogenic background and suggest that such QTLs could be utilized in the breeding of high-yielding rice varieties.

关键词： 1000-grain weight minor effect quantitative trait locus rice (Oryza sativa L.)

Identification and Validation of a Major quantitative trait locus for Slow-rusting Resistance to Stripe Rust in Wheat

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Journal of Integrative Plant Biology 2012年第5期54卷 330-344页

作者： Xiaohua Cao Jianghong Zhou Xiaoping Gong Guangyao Zhao Jizeng Jia Xiaoquan Qi Key Laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of SciencesBeijing 100093China Graduate University of Chinese Academy of Sciences Beijing 100049China Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China These authors contributed equally to this article.

Stripe （yellow） rust, caused by Puccinia striiformis Westend. f. sp. tritici Eriks （Pst）, is one of the most important wheat （Triticum aestivum L.） diseases and causes significant yield losses. A recombinant inbred （RI） population derived from a cross between Yanzhan 1 and Xichang 76-9 cultivars was evaluated for resistance to wheat stripe rust strain CYR32 at both the seedling and adult plant stages. Four resistance quantitative trait loci （QTLs） were detected in this population, in which the major one, designated as Yrql, was mapped on chromosome 2DS. The strategy of using the Brachypodium distachyon genome, wheat expressed sequence tags and a draft DNA sequences （scaffolds） of the D-genome （Aegilops tauschfi Coss.） for the development of simple sequence repeat （SSR） markers was successfully used to identify 147 SSRs in hexaploid wheat. Of the 19 polymorphic SSRs in the RI population, 17 SSRs were mapped in the homeologous group 2 chromosomes near Yrql region and eight SSRs were genetically mapped in the 2.7 cM region of Yrql, providing abundant DNA markers for fine-mapping of Yrql and marker-assisted selection in wheat breeding program. The effectiveness of Yrql was validated in an independent population, indicating that this resistance QTL can be successfully transferred into a susceptible cultivar for improvement of stripe rust resistance.

关键词： quantitative trait locus slow-rusting stripe rust wheat.

Generalized fiducial methods for testing quantitative trait locus effects in genetic backcross studies

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Statistical Theory and Related Fields 2022年第2期6卷 148-160页

作者： Pengcheng Ren Guanfu Liu Xiaolong Pu Yan Li KLATASDS-MOE School of StatisticsEast China Normal UniversityShanghaiPeople’s Republic of China School of Statistics and Information Shanghai University of International Business and EconomicsShanghaiPeople’s Republic of China

In this paper,we propose generalized fiducial methods and construct four generalized p-values to test the existence of quantitative trait locus effects under phenotype distributions from a location-scale *** with the likelihood ratio test based on simulation studies,our methods perform better at controlling type I errors while retaining comparable power in cases with small or moderate sample *** four generalized fiducial methods support varied sce-narios:two of them are more aggressive and powerful,whereas the other two appear more conservative and robust.A real data example involving mouse blood pressure is used to illustrate our proposed methods.

关键词： Generalized fiducial inference quantitative trait locus mixture model Gibbs algorithm likelihood ratio test

Identification of Rice QTLs for Important Agronomic traits with Long-Kernel CSSL-Z741 and Three SSSLs

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Rice science 2020年第5期27卷 414-422,I0025页

作者： Wang Hui Zhang Jiayu Naz Farkhanda Li Juan Sun Shuangfei He Guanghua Zhang Ting Ling Yinghua Zhao Fangming Rice Research Institute/College of Agronomy and Biotechnology Southwest UniversityChongqing 400715China

Rice kernel shape affects kernel quality(appearance) and yield(1000-kernel weight) and therefore is an important agronomic trait, but its inheritance is complicated. We identified a long-kernel rice chromosome segment substitution line(CSSL), Z741, derived from Nipponbare as a recipient and Xihui 18 as a donor parent. Z741 has six substitution segments distributed on rice chromosomes 3, 6, 7, 8 and 12 with an average replacement length of 5.82 Mb. Analysis of a secondary F2 population from a cross between Nipponbare and Z741 identified 20 QTLs for important agronomic traits. The kernel length of Z741 is controlled by a major QTL(qKL3) and a minor QTL(qKL7). Candidate gene prediction and sequencing indicated that qKL3 may be an allele of OsPPKL1, which encodes a protein phosphatase implicated in brassinosteroid signaling, and qKL7 is an unreported QTL. Finally, we validated eight QTLs(qKL3, qKL7, qRLW3-1, qRLW7, qPH3-1, qKWT3, qKWT7 and qNPB6) using three selected singlesegment substitution lines(SSSLs), S1, S2 and S3. Also, we detected five QTLs(qKL6, qKW3, qKW7, qKW6 and qRLW6) in S1, S2 and S3, which were not found in the Nipponbare/Z741 F2 population. However, qNPB3, qNPB7 and qPL3 QTLs were not validated by the three SSSLs in 2019, suggesting that minor QTLs are susceptible to environmental factors. These results lay the foundation for studying the biodiversity of kernal length and molecular breeding of different kernel types.

关键词： chromosome segment substitution line single-segment substitution line kernel shape quantitative trait locus rice

QTL and candidate genes associated with common bacterial blight resistance in the common bean cultivar Longyundou 5 from China

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The Crop Journal 2016年第5期4卷 344-352页

作者： Jifeng Zhu Jing Wu Lanfen Wang Matthew W.Blair Zhendong Zhu Shumin Wang Institute of Crop Science Chinese Academy of Agricultural Sciences Department of Agriculture & Environment Tennessee State University

Common bacterial blight(CBB), caused by Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans(Xff), is a worldwide disease of common bean(Phaseolus vulgaris L.).Longyundou 5, a Chinese cultivar in the Mesoamerican gene pool of common bean, displays resistance to the Xff strain XSC3-1. To identify the genetic mechanisms behind this resistance,we crossed Long 5 with a susceptible genotype to develop a mapping population of F2 *** resistance to CBB was identified at 14 and 21 days after inoculation with Xff strain XSC3-1.A major QTL at 14 and 21 days after inoculation was mapped on chromosome Pv10 with LOD scores of 6.41 and 5.35, respectively. This locus was associated with SAP6, a previouslyidentified and much-used dominant marker, but in a 4.2 cM interval between new codominant markers BMp10s174 and BMp10s244. Ten candidate genes were found between markers BMp10s174 and BMp10s244 on chromosome Pv10 and could encode defense response proteins responding to CBB pathogens. Four pairs each of epistatic QTL for CBB resistance were detected at 14 and 21 days after inoculation. Phenotypic variation explained by the epistatic QTL ranged from 7.19% to 12.15% and 7.72% to 8.80% at 14 and 21 days after inoculation, respectively. These results confirmed the importance of epistasis in CBB resistance in common bean. The adjacent markers found may be more efficient for marker assisted selection in common bean breeding for CBB resistance owing to their closer linkage to the target QTL.

关键词： Common bean(Phaseoius vulgaris L.) Common bacterial blight quantitative trait locus Days after inoculation

QTL mapping for grain number per spikelet in wheat using a high-density genetic map

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The Crop Journal 2021年第5期9卷 1108-1114页

作者： Yu Lin Xiaojun Jiang Haiyan Hu Kunyu Zhou Qing Wang Shifan Yu Xilan Yang Zhiqiang Wang Fangkun Wu Shihang Liu Caixia Li Mei Deng Jian Ma Guangdeng Chen Yuming Wei Youliang Zheng Yaxi Liu State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China WenjiangChengdu 611130SichuanChina Triticeae Research Institute Sichuan Agricultural UniversityWenjiangChengdu 611130SichuanChina School of Life Science and Technology Henan Institute of Science and TechnologyXinxiang 453003HenanChina College of Resources Sichuan Agricultural UniversityWenjiangChengdu 611130SichuanChina

Grain number per spikelet (GNS) is a key determinant of grain yield in wheat.A recombinant inbred line population comprising 300 lines was developed from a cross between a high GNS variety H461 and Chinese Spring from which the reference genome assembly of bread wheat was *** parents and the recombinant inbred lines were genotyped using the wheat 55K single nucleotide polymorphism(SNP) array.A high-density genetic map containing 21,197 SNPs was *** markers covered each of the 21 chromosomes with a total linkage distance of 3792.71 c *** of these markers in this linkage map were highly consistent with their physical locations in the genome assembly of Chinese *** two parents and the whole RIL population were assessed for GNS in two consecutive years at two different *** on multi-environment phenotype data and best liner unbiased prediction values,three quantitative trait loci (QTL) for GNS were *** of them located on chromosomes 2B and the other two on *** variation explained by these loci varied from 3.07%to26.57%.One of these QTL,***-2D-2,was identified in each of all trials *** on the best linear unbiased prediction values,this locus explained 19.59%–26.57%of phenotypic variation.A KASP(Kompetitive Allele-Specific PCR) marker closely linked with this locus was generated and used to validate the effects of this locus in three different genetic *** identified QTL and the KASP marker developed for it will be highly valuable in fine-mapping the locus and in exploiting it for markerassisted selection in wheat breeding programs.

关键词： Chinese Spring Grain number per spikelet High-density map KASP quantitative trait locus

A stable and major QTL region on chromosome 2 conditions pod shape in cultivated peanut(Arachis hyopgaea L.)

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Journal of Integrative Agriculture 2023年第8期22卷 2323-2334页

作者： ZHANG Sheng-zhong HU Xiao-hui WANG Fei-fei CHU Ye YANG Wei-qiang XU Sheng WANG Song WU Lan-rong YU Hao-liang MIAO Hua-rong FU Chun CHEN Jing Shandong Peanut Research Institute Qingdao 266100P.R.China Department of Horticulture University of Georgia Tifton CampusTiftonGA 31793the United States Anhui General Station of Agricultural Technology Extension Hefei 230001P.R.China Anhui Academy of Agricultural Sciences Hefei 230001P.R.China Qingdao Agricultural Technology Extension Center Qingdao 266071P.R.China Yantai Fenglin Foodstuff Co. Ltd.Ltd.Yantai 264108P.R.China Weifang Academy of Agricultural Sciences Weifang 261071P.R.China

Peanut pod shape is a heritable trait which affects the market acceptance of in-shell peanut *** order to determine the genetic control of pod shape,six component traits of pod shape(pod length,pod width,pod length/width ratio,pod roundness,beak degree and constriction degree)were measured using an image-based phenotyping method.A recombinant inbred line(RIL)population consisting of 181 lines was phenotyped across three *** distributions and transgressive segregations were demonstrated in all measured traits and *** correlations were found among most component traits with broad-sense heritability ranging from 0.87 to *** trait locus(QTL)analysis yielded 26 additive QTLs explaining 3.79 to 52.37%phenotypic variations.A novel,stable and major QTL region conditioning multiple shape features was detected on chromosome 2,which spans a 10.81-Mb genomic region with 543 putative *** analysis revealed several candidate genes in this *** addition,73 pairs of epistatic interactions involving 92 loci were identified for six component traits explaining 0.94–6.45%phenotypic *** results provide new genetic loci to facilitate genomics-assisted breeding of peanut pod shape.

关键词： peanut pod shape quantitative trait locus additive effect epistasis

Genetic mapping of quantitative trait loci associated with β-amylase and limit dextrinase activities and β-glucan and protein fraction contents in barley

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2009年第11期10卷 839-846页

作者： Kang WEI Da-wei XUE You-zong HUANG Xiao-li JIN Fei-bo WU Guo-ping ZHANG Department of Agronomy Zhejiang University Hangzhou 310029 China College of Life and Environment Sciences Hangzhou Normal University Hangzhou 310036 China College of Agriculture Guangxi University Nanning 530004 China

High malting quality of barley （Hordeum vulgare L.） relies on many traits, such as β-amylase and limit dextrinase activities and β-glucan and protein fraction contents. In this study, interval mapping was utilized to detect quantitative trait loci （QTLs） affecting these malting quality parameters using a doubled haploid （DH） population from a cross of CM72 （six-rowed） by Gairdner （two-rowed） barley cultivars. A total of nine QTLs for eight traits were mapped to chromosomes 3H, 4H, 5H, and 7H. Five of the nine QTLs mapped to chromosome 3H, indicating a possible role ofloci on chromosome 3H on malting quality. The phenotypic variation accounted by individual QTL ranged from 8.08% to 30.25%. The loci of QTLs for D-glucan and limit dex- trinase were identified on chromosomes 4H and 5H, respectively. QTL for hordeins was coincident with the region of silica eluate （SE） protein on 3HS, while QTLs for albumins, globulins, and total protein exhibited overlapping. One locus on chromosome 3H was found to be related to （J-amylase, and two loci on chromosomes 5H and 7H were found to be associated with glutelins. The identification of these novel QTLs controlling malting quality may be useful for marker-assisted selection in improving barley malting quality.

关键词： Barley (Hordeum vulgate L.) quantitative trait locus O-amylase Limit dextrinase β-glucan Protein fraction