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Genetic architecture of maize yield traits dissected by QTL mapping and GWAS in maize

The Crop Journal 2022年第2期10卷 436-446页

作者： Xiao Zhang Zhiyong Ren Bowen Luo Haixu Zhong Peng Ma Hongkai Zhang Hongmei Hu Yikai Wang Haiying Zhang Dan Liu Ling Wu Zhi Nie Yonghui Zhu Wenzhu He Suzhi Zhang Shunzong Su Yaou Shen Shibin Gao Maize Research Institute Sichuan Agricultural UniversityChengdu 611130SichuanChina Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region Ministry of AgricultureChengdu 611130SichuanChina Guangxi Qingqing Agricultural Technology CO. LTD.Nanning 530000GuangxiChina Biotechnology and Nuclear Technology Research Institute Sichuan Academy of Agricultural SciencesChengdu 610066SichuanChina Crop Research Institute Sichuan Academy of Agricultural SciencesChengdu 610066SichuanChina State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China Chengdu 611130SichuanChina g College of Agronomy Sichuan Agricultural UniversityChengdu 611130SichuanChina

The study of yield traits can reveal the genetic architecture of grain yield for improving maize *** this study, an association panel comprising 362 inbred lines and a recombinant inbred line population derived from X178 × 9782 were used to identify candidate genes for nine yield traits. High-priority overlap(HPO) genes, which are genes prioritized in a genome-wide association study(GWAS), were investigated using coexpression networks. The GWAS identified 51 environmentally stable SNPs in two environments and 36 pleiotropic SNPs, including three SNPs with both attributes. Seven hotspots containing 41 trait-associated SNPs were identified on six chromosomes by permutation. Pyramiding of superior alleles showed a highly positive effect on all traits, and the phenotypic values of ear diameter and ear weight consistently corresponded with the number of superior alleles in tropical and temperate germplasm. A total of 61 HPO genes were detected after trait-associated SNPs were combined with the coexpression networks. Linkage mapping identified 16 environmentally stable and 16 pleiotropic *** SNPs that were located in QTL intervals were assigned as consensus SNPs for the yield *** the candidate genes predicted by our study, some genes were confirmed to function in seed development. The gene Zm00001 d016656 encoding a serine/threonine protein kinase was associated with five different traits across multiple environments. Some genes were uniquely expressed in specific tissues and at certain stages of seed development. These findings will provide genetic information and resources for molecular breeding of maize grain yield.

关键词： Maize yield traits Genome-wide association study(GWAS) Quantitative trait locus(QTL) Coexpression networks

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Auxin signaling module OsSK41-OsIAA10-OsARF regulates grain yield traits in rice

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Journal of Integrative Plant Biology 2023年第7期65卷 1753-1766页

作者： Fuying Ma Fan Zhang Yu Zhu Dengyong Lan Peiwen Yan Ying Wang Zejun Hu Xinwei Zhang Jian Hu Fuan Niu Mingyu Liu Shicong He Jinhao Cui Xinyu Yuan Ying Yan Shujun Wu Liming Cao Hongwu Bian Jinshui Yang Zhikang Li Xiaojin Luo State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology School of Life SciencesFudan UniversityShanghai 200438China Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China College of Agronomy Anhui Agricultural UniversityHefei 230036China Institute of Crop Breeding and Cultivation Shanghai Academy of Agricultural SciencesShanghai 201403China Institute of Genetics and Regenerative Biology Key Laboratory for Cell and Gene Engineering of Zhejiang ProvinceCollege of Life SciencesZhejiang UniversityHangzhou 310058China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518100China

Auxin is an important phytohormone in plants, and auxin signaling pathways in rice play key roles in regulating its growth, development, and productivity. To investigate how rice grain yield traits are regulated by auxin signaling pathways and to facilitate their application in rice improvement, we validated the functional relationships among regulatory genes such as OsIAA10, OsSK41, and OsARF21 that are involved in one of the auxin(OsIAA10) signaling pathways. We assessed the phenotypic effects of these genes on several grain yield traits across two environments using knockout and/or overexpression transgenic *** on the results, we constructed a model that showed how grain yield traits were regulated by OsIAA10 and OsTIR1, OsAFB2, and OsSK41 and OsmiR393 in the OsSK41-OsIAA10-OsARF module and by OsARF21 in the transcriptional regulation of downstream auxin response genes in the OsSK41-OsIAA10-OsARF module. The population genomic analyses revealed rich genetic diversity and the presence of major functional alleles at most of these loci in rice populations. The strong differentiation of many major alleles between Xian/indica and Geng/japonica subspecies and/or among modern varieties and landraces suggested that they contributed to improved productivity during evolution and breeding. We identified several important aspects associated with the genetic and molecular bases of rice grain and yield traits that were regulated by auxin signaling *** also suggested rice auxin response factor(OsARF) activators as candidate target genes for improving specific target traits by overexpression and/or editing subspecies-specific alleles and by searching and pyramiding the ‘best' gene allelic combinations at multiple regulatory genes in auxin signaling pathways in rice breeding programs.

关键词： allele evolution auxin signaling pathways OsARFs OsIAA10 yield traits

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Barley FASCIATED EAR genes determine inflorescence meristem size and yield traits

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The Crop Journal 2023年第3期11卷 679-691页

作者： Chengyu Wang Xiujunan Yang Yueya Zhang Chaoqun Shen Jin Shi Chongjing Xia Taohong Fang Qiang Tu Ling Li Xinli Zhou Dabing Zhang Gang Li School of Life Sciences and Engineering Southwest University of Science and TechnologyMianyang 629000SichuanChina School of Agriculture Food and WineWaite Research InstituteThe University of AdelaideAdelaide 5005SAAustralia School of Life Science and Biotechnology Shanghai Jiao Tong UniversityShanghai 200240China Department of Plant Pathology College of Plant ProtectionNanjing Agricultural UniversityNanjing 210095JiangsuChina

In flowering plants,the inflorescence meristem(IM)provides founder cells to form successive floral meristems,which are precursors of fruits and *** activity and developmental progression of IM are thus critical for yield production in seed *** some cereals,such as rice(Oryza sativa)and maize(Zea mays),the size of undifferentiated IM,which is located at the inflorescence apex,is positively associated with yield traits such as spikelet ***,the relationship between IM size and yieldrelated spike traits remains unknown in the Triticeae *** we report that IM size has a negative correlation with yield traits in barley(Hordeum vulgare).Three FASCIATED EAR(FEA)orthologs,HvFEA2,HvFEA3,and HvFEA4,regulate IM size and spike morphogenesis and ultimately affect yield *** HvFEAs genes are highly expressed in developing spikes,and all three loss-of-function mutants exhibit enlarged IM size,shortened spikes,and reduced spikelet number,which may lead to reduced grain *** variations identified in HvFEAs indicate selection events during barley *** further reveal that HvFEA4,as a transcription factor,potentially targets multiple pathways during reproductive development,including transcriptional control,phytohormone signaling,and redox *** roles of barley FEA genes in limiting IM size and promoting spikelet formation suggest the potential of increasing yield by manipulating IM activity.

关键词： Inflorescence meristem yield traits FASCIATED EAR genes Gene expression Barley

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Dissection of QTLs for yield traits on the Short Arm of Rice Chromosome 6

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Agricultural Sciences in China 2008年第5期7卷 513-520页

作者： DU Jing-hong FAN Ye-yang WU Ji-rong ZHUANG Jie-yun Chinese National Center for Rice Improvement/State Key Laboratory of Rice Science China National Rice Research Institute Hangzhou310006 P.R.China

This study was undertaken to dissect quantitative trait loci （QTLs） controlling yield traits on the short arm of rice chromosome 6. A residual heterozygous line that carries a heterozygous segment extending from RM587 to RM19784 on the short arm of rice chromosome 6 was selected from an F7 population of the indica rice cross Zhenshan 97B/Milyang 46. An F2：3 population consisting of 221 lines was derived and grown in two trial sites. Six yield traits including number of panicles per plant, number of filled grains per panicle, total number of spikelets per panicle, spikelet fertility, 1 000-grain weight, and grain yield per plant were measured. An SSR marker linkage map was constructed and employed to determine QTLs for yield traits with Windows QTL Cartographer 2.5. QTLs were detected in the target interval for all the traits analyzed except NP, with phenotypic variance explained by a single QTL ranging between 6.3% and 35.2%. Most of the QTLs for yield components acted as additive QTLs, while the three QTLs for grain yield had dominance degrees of 1.65, 0.84, and -0.42, respectively. It was indicated that three or more QTLs for yield traits were located in the target region. The genetic action mode, the direction of the QTL effect, and the magnitude of the QTL effect varied among different QTLs for a given trait, and among QTLs for different traits that were located in the same interval.

关键词： yield traits residual heterozygous line quantitative trait locus short arm of chromosome 6 rice (Oryza sativa L.)

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Quantitative Trait Loci for Heading Date and Their Relationship with Genetic Control of yield traits in Rice (Oryza sativa)

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Rice science 2013年第1期20卷 1-12页

作者： GUO Liang ZHANG Zhen-hua ZHUANG Jie-yun Chinese National Center for Rice Improvement/State Key Laboratory of Rice Biology China National Rice Research Institute

Grain yield and heading date are key factors determining the commercial potential of a rice variety. Mapping of quantitative trait loci （QTLs） in rice has been advanced from primary mapping to gene cloning, and heading date and yield traits have always attracted the greatest attention. In this review, genomic distribution of QTLs for heading date detected in populations derived from intra-specific crosses of Asian cultivated rice （Oryza sativa） was summarized, and their relationship with the genetic control of yield traits was analyzed. The information could be useful in the identification of QTLs for heading date and yield traits that are promising for the improvement of rice varieties.

关键词： rice heading date yield traits quantitative trait locus gene

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Dissection of QTLs for yield traits Using Near Isogenic Lines Derived from Residual Heterozygous Lines in Rice

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Rice science 2008年第4期15卷 259-266页

作者： Jing-hong DU Ye-yang FAN Lei WANG Jie-yun ZHUANG China National Rice Research Institute Hangzhou 310006 China

Three residual heterozygous lines (RHLs) carrying heterozygous segments in the intervals RM587–RM225, RM204–RM6119 and RM6119–RM402 on the short arm of rice chromosome 6, respectively, were selected from a rice population derived from an RHL for the interval RM587–RM402. Ten maternal homozygotes, 10 paternal homozygotes and 20 heterozygotes were selected from each of the F2 populations derived from the three RHLs. The three sets of near isogenic lines (NILs) were grown to detect the grain yield per plant, number of panicles per plant, number of filled grains per panicle and 1000-grain weight. With analysis on the phenotypic differences among the three genotype groups in each NIL set and those among overlapping chromosome segment substitution lines, three QTLs for number of filled grains per panicle and two QTLs for grain yield per plant were resolved. They were located in the intervals ranging from 0.66 Mb to 2.49 Mb. The additive effect was higher than the dominance effect at each locus. The allele for increasing the trait value was derived from the paternal parent at qNFGP6-1, and from the maternal alleles at other QTLs. Based on the present study, an approach for constructing new genetic resource to facilitate fine mapping of QTLs in rice was proposed.

关键词： residual heterozygous line near isogenic line quantitative trait locus yield traits rice (Oryza sativa)

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QTL Mapping and Epistasis Analysis for yield traits in an RIL Population of Rice(Oryza sativa L.)

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Agricultural Sciences in China 2003年第11期2卷 1179-1186页

作者： CAO Li-yong, ZHAN Xiao-deng, ZHUANG Jie-yun, ZHENG Kang-le and CHENG Shi-hua(National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006 , P. R. China) National Center for Rice Improvement China National Rice Research Institute Hangzhou 310006 P.R. China

A genetic linkage map consisting of 168 DNA markers was constructed based on a recombinant inbred line(RID population derived from a cross between a high yielding indica variety, Zhong156, and a low yielding indica variety, Gumeil. The markers on the linkage map were distributed on all 12 chromosomes and covered 1 447. 9 cM of the genome. The parents and 304 RILs were grown in China National Rice Research Institute(CNRRI), Hangzhou, China, in 2001, over two seasons in a randomized block design. The statistic software of QTL Mapper 1.01 was applied to detect quantitative trait loci(QTLs)and additive by environment(AE)interactions for yield traits, including panicle length, number of panicles per plant, number of spikelets per panicle, number of filled grains per panicle, fertility and kilo-grain weight. A total of 30 QTLs with significant additive effects located on all chromosomes, except chromosomes 5 and 9, and two QTLs with significant AE interactions, were detected. Thirty-one interactions of QTLs showing significant additive by additive epistatic effects for yield traits were also detected. Genetic contributions were generally lower for QTLs showing epistatic effects compared with QTLs showing additive effects. No significant interactions between epistasis and environment were detected.

关键词： yield traits QTLs Additive effect Epistasis Oryza sativa L.

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Combining Ability Analysis on yield traits of Recombinant Inbred Lines in Hybrid Rice

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Agricultural Science & Technology 2015年第9期16卷 1877-1882页

作者：曹应江游书梅郑家奎蒋开锋张涛杨莉杨乾华万先齐罗婧李昭祥高磊四川省农业科学院水稻高粱研究所/国家水稻改良中心泸州分中心/农业部西南水稻生物学与遗传育种重点实验室四川德阳618000

A population of 140 recombinant inbred lines at F8 generation were obtained after seven successive generations of self-pollination using single seed descent（SSD） method from the F2 hybrids of three-line restorers Luhui 8258 with high combining ability and Yanghui 34. Then, the 140 inbred lines obtained above and their parents Luhui 8258 and Yanghui 34 were crossed with three different types of cyto-plasmic male sterile（CMS） lines（Gang 46 A, Ⅱ-32 A and Lu 98A） according to NCⅡ design. The resulting 426 combinations were planted at Deyang and Suining bases to test the combining ability and inheritance of five yield traits： yield per plant, panicle number per plant, filled grain number per panicle, seed setting rate and 1 000-grain weight. The results showed that the variances of both general and specific combining abilities of the five traits all reached a significant or extremely significant level at the two sites. The broad and narrow heritability of the yield traits（except 1 000-grain weight whose broad and narrow heritability were both over70%） were all below 50% at the two experimental bases, suggesting that the four traits were easily subjected to environment influence. Very significant positive correlation of general combining ability was found between yield per plant and other traits except 1 000-grain weight. The general combining ability variance showed a normal distribution among the recombinant inbred lines at two sites, right in line with inheritance of quantitative traits. So, the genes controlling rice general combining ability can be targeted by QTL mapping.

关键词： Hybrid rice Recombinant inbred lines yield traits Combining ability

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Effects of Aphelenchoides besseyi Infection on yield traits of Different Rice Varieties (Lines)

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Agricultural Science & Technology 2016年第5期17卷 1173-1176,1180页

作者：朱镇于新张亚东陈涛赵庆勇周丽慧姚姝赵春芳赵凌王才林江苏省农业科学院粮食作物研究所江苏省优质水稻工程技术研究中心国家水稻改良中心南京分中心苏南京210014

[Objective] This study aimed to reveal the effects of Aphelenchoides besseyi infection on different rice varieties（lines）.[Method] By field observation and indoor phenotypic investigation,four conventional japonica rice varieties（lines） and japonica rice restorer line R161 under natural onset conditions were observed and analyzed.[Result] After being infected by ***,different rice varieties（lines）exhibited various ***,Ning 1707,Ning 1818,Zhendao 88 and Nanjing 9108 had withered leaf tips and exhibited the symptoms of ＂small grains and erect panicles＂;japonica rice restorer line R161 only had withered leaf tips without symptoms of ＂small grains and erect panicles＂,and the withering symptoms occurred in flag leaf tip,whole flag leaf and top second leaf,*** being infected by ***,all the experimental materials could sprout normally,but their plant height,panicle length,seed-setting rate and 1 000-grain weight were affected to varying *** addition,after being infected by ***,various symptomatic tissues of R161 exerted different effects on rice ***,panicles with withered and twisted whole flag leaf were most affected.[Conclusion] This study provided the basis for further exploration of the damages of *** infection to rice and development of corresponding control measures.

关键词： Rice(Oryza sativa L.) Aphelenchoides besseyi Small grains and erect panicles yield traits

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Down-regulation of GY6 gene resulted in improved yield traits in indica rice

Down-regulation of GY6 gene resulted in improved yield trait...

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2014年中国作物学会学术年会

作者： Ma Huan Ying Jiezheng Fan Yeyang Zhu Yujun Huang Derun Zhuang Jieyun Chinese National Center for Rice Improvement/State Key Laboratory of Rice Biology China National Rice Research Institute College of life science Hebei Normal University

GY6 is a pleotropic gene conditioning heading date,number of grains per panicle,plant height and grain *** we report that decreased expression of GY6 caused by RNA interference(RNAi)technology could improve yield traits in *** vector was constructed with a double T-DNA binary vector ’p1102’ and transformed into a well-known indica cytoplasm male sterile restorer line ’Minghui86’mediated by *** expression of GY6 gene was validated by real-time polymerase chain reaction(PCR).Southern blot analysis of the transgenic rice was performed to confirm the presence and copy number of the GY6 RNAi *** asymmetric interlaced PCR was employed to determine the insertion sites of GY6 RNAi structure on rice *** with the wild type ’Minghui86’,heading date of the transgenic lines was significantly delayed for 13-17 days in T1 *** homozygous transgenic lines,TGY61,TGY62,TGY63,and the wild type were selected for a randomized compete design with three replications in the field in Zhejiang *** of rice inflorescence development with a stereomicroscope indicated that down-regulation of GY6 gene significantly prolonged the basic vegetative growth period of the transgenic lines,but showed a little effect on the regulation of the duration of panicle *** with the wild type,the transgenic lines,TGY61,TGY62 and TGY63 increased grain yield per plant by 6.5-6.9g.

关键词： rice(Oryza sativa) GY6 heading date yield traits gene regulation

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