QTL mapping of yield components and kernel traits in wheat cultivars TAM 112 and Duster

In the Southern Great Plains, wheat cultivars have been selected for a combination of outstanding yield and drought tolerance as a long-term breeding goal. To understand the underlying genetic mechanisms, this study aimed to dissect the quantitative trait loci (QTL) associated with yield components and kernel traits in two wheat cultivars `TAM 112' and `Duster' under both irrigated and dryland environments. A set of 182 recombined inbred lines (RIL) derived from the cross of TAM 112/Duster were planted in 13 diverse environments for evaluation of 18 yield and kernel related traits. High-density genetic linkage map was constructed using 5,081 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). QTL mapping analysis detected 134 QTL regions on all 21 wheat chromosomes, including 30 pleiotropic QTL regions and 21 consistent QTL regions, with 10 QTL regions in common. Three major pleiotropic QTL on the short arms of chromosomes 2B (57.5 - 61.6 Mbps), 2D (37.1 - 38.7 Mbps), and 7D (66.0 - 69.2 Mbps) colocalized with genes Ppd-B1, Ppd-D1, and FT-D1, respectively. And four consistent QTL associated with kernel length (KLEN), thousand kernel weight (TKW), plot grain yield (YLD), and kernel spike-1 (KPS) (Qklen.tamu.1A.325, Qtkw.tamu.2B.137, Qyld.tamu.2D.3, and Qkps.tamu.6A.113) explained more than 5% of the phenotypic variation. QTL Qklen.tamu.1A.325 is a novel QTL with consistent effects under all tested environments. Marker haplotype analysis indicated the QTL combinations significantly increased yield and kernel traits. QTL and the linked markers identified in this study will facilitate future marker-assisted selection (MAS) for pyramiding the favorable alleles and QTL map-based cloning.

[1]  Mingming Xin,et al.  A single nucleotide deletion in the third exon of FT‐D1 increases the spikelet number and delays heading date in wheat (Triticum aestivum L.) , 2022, Plant biotechnology journal.

[2]  Mingming Xin,et al.  A natural variation in Ribonuclease H-like gene underlies Rht8 to confer "Green Revolution" trait in wheat. , 2022, Molecular plant.

[3]  Q. Xue,et al.  Genome-wide QTL mapping of yield and agronomic traits in two widely adapted winter wheat cultivars from multiple mega-environments , 2021, PeerJ.

[4]  Jiaqiang Sun,et al.  Transcription factors PILs directly interact with SPLs and repress tillering/branching in plants. , 2021, The New phytologist.

[5]  Muhammad Adeel Hassan,et al.  Rht24b, an ancient variation of TaGA2ox-A9, reduces plant height without yield penalty in wheat. , 2021, The New phytologist.

[6]  G. Brown-Guedira,et al.  Identification and characterization of a natural polymorphism in FT-A2 associated with increased number of grains per spike in wheat , 2021, TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik.

[7]  J. Dubcovsky,et al.  WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat , 2021, bioRxiv.

[8]  Yaxi Liu,et al.  Genetic Mapping and Validation of Loci for Kernel-Related Traits in Wheat (Triticum aestivum L.) , 2021, Frontiers in Plant Science.

[9]  M. Lillemo,et al.  Identification of eight QTL controlling multiple yield components in a German multi-parental wheat population, including Rht24, WAPO-A1, WAPO-B1 and genetic loci on chromosomes 5A and 6A , 2021, Theoretical and Applied Genetics.

[10]  E. Akhunov,et al.  QTL mapping for grain yield and three yield components in a population derived from two high-yielding spring wheat cultivars , 2021, Theoretical and Applied Genetics.

[11]  P. Luo,et al.  Utilization of a Wheat55K SNP array-derived high-density genetic map for high-resolution mapping of quantitative trait loci for important kernel-related traits in common wheat , 2021, Theoretical and Applied Genetics.

[12]  Li Tao,et al.  Integration of meta-QTL discovery with omics: Towards a molecular breeding platform for improving wheat resistance to Fusarium head blight , 2020 .

[13]  Yunfeng Xu,et al.  Identification and validation of quantitative trait loci for kernel traits in common wheat (Triticum aestivum L.) , 2020, BMC plant biology.

[14]  Charles D. Johnson,et al.  Genetic dissection of end‐use quality traits in two widely adapted wheat cultivars ‘TAM 111’ and ‘TAM 112’ , 2020 .

[15]  P. Pérez-Rodríguez,et al.  META-R: A software to analyze data from multi-environment plant breeding trials , 2020, The Crop Journal.

[16]  Shancen Zhao,et al.  Major genomic regions responsible for wheat yield and its components as revealed by meta-QTL and genotype–phenotype association analyses , 2020, Planta.

[17]  Z. Li,et al.  Appraising the Genetic Architecture of Kernel Traits in Hexaploid Wheat Using GWAS , 2020, International journal of molecular sciences.

[18]  Charles D. Johnson,et al.  Genome wide identification of QTL associated with yield and yield components in two popular wheat cultivars TAM 111 and TAM 112 , 2020, bioRxiv.

[19]  G. Bai,et al.  High-Resolution Genome-Wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat. , 2020, Molecular plant.

[20]  Ji-chun Tian,et al.  A major and stable QTL controlling wheat thousand grain weight: identification, characterization, and CAPS marker development , 2020, Molecular Breeding.

[21]  P. Langridge,et al.  Green revolution "stumbles" in a dry environment: Dwarf wheat with Rht genes fails to produce higher grain yield than taller plants under drought. , 2020, Plant, cell & environment.

[22]  J. Poland,et al.  Incorporating Genome-Wide Association Mapping Results Into Genomic Prediction Models for Grain Yield and Yield Stability in CIMMYT Spring Bread Wheat , 2020, Frontiers in Plant Science.

[23]  Xin-ming Yang,et al.  Dissection of Superior Alleles for Yield-Related Traits and Their Distribution in Important Cultivars of Wheat by Association Mapping , 2020, Frontiers in Plant Science.

[24]  Zhonghu He,et al.  Genetic architecture underpinning yield component traits in wheat , 2020, Theoretical and Applied Genetics.

[25]  J. Jia,et al.  QTL mapping for yield-related traits in wheat based on four RIL populations , 2020, Theoretical and Applied Genetics.

[26]  Jiang Li,et al.  Dissection of genetic factors underlying grain size and fine mapping of QTgw.cau-7D in common wheat (Triticum aestivum L.) , 2020, Theoretical and Applied Genetics.

[27]  P. Ingvarsson,et al.  Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs , 2019, BMC Plant Biology.

[28]  D. An,et al.  TaDA1, a conserved negative regulator of kernel size, has an additive effect with TaGW2 in common wheat (Triticum aestivum L.) , 2019, Plant biotechnology journal.

[29]  Y. Yue,et al.  The potential global distribution and dynamics of wheat under multiple climate change scenarios. , 2019, The Science of the total environment.

[30]  Jiang Li,et al.  Dissection of genetic factors underlying grain size and fine mapping of QTgw.cau-7D in common wheat (Triticum aestivum L.) , 2019, Theoretical and Applied Genetics.

[31]  Philomin Juliana,et al.  Improving grain yield, stress resilience and quality of bread wheat using large-scale genomics , 2019, Nature Genetics.

[32]  Yaxi Liu,et al.  Identification of quantitative trait loci for kernel traits in a wheat cultivar Chuannong16 , 2019, BMC Genetics.

[33]  F. Wang,et al.  TaD27‐B gene controls the tiller number in hexaploid wheat , 2019, Plant biotechnology journal.

[34]  G. Bai,et al.  Gene editing of the wheat homologs of TONNEAU1‐recruiting motif encoding gene affects grain shape and weight in wheat , 2019, The Plant journal : for cell and molecular biology.

[35]  J. Anderson,et al.  Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping , 2019, Theoretical and Applied Genetics.

[36]  Hong Zhao,et al.  Cloning, characterization of TaGS3 and identification of allelic variation associated with kernel traits in wheat (Triticum aestivum L.) , 2019, BMC Genetics.

[37]  M. Reynolds,et al.  Genetic dissection of drought and heat‐responsive agronomic traits in wheat , 2019, Plant, cell & environment.

[38]  Jindong Liu,et al.  Genetic architecture of grain yield in bread wheat based on genome-wide association studies , 2019, BMC Plant Biology.

[39]  M. Reynolds,et al.  Genome-wide association study reveals genomic regions controlling root and shoot traits at late growth stages in wheat , 2019, Annals of botany.

[40]  Lingli Dong,et al.  Molecular characterization of a novel TaGL3-5A allele and its association with grain length in wheat (Triticum aestivum L.) , 2019, Theoretical and Applied Genetics.

[41]  F. Chen,et al.  Genome-wide association study revealed that the TaGW8 gene was associated with kernel size in Chinese bread wheat , 2019, Scientific Reports.

[42]  A. Mosquna,et al.  GNI-A1 mediates trade-off between grain number and grain weight in tetraploid wheat , 2019, Theoretical and Applied Genetics.

[43]  J. Dubcovsky,et al.  FLOWERING LOCUS T2 regulates spike development and fertility in temperate cereals , 2018, Journal of experimental botany.

[44]  C. Sneller,et al.  Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia , 2018, bioRxiv.

[45]  F. Wang,et al.  A Genome-Wide Association Study of Wheat Spike Related Traits in China , 2018, Front. Plant Sci..

[46]  Jonathan D. G. Jones,et al.  Shifting the limits in wheat research and breeding using a fully annotated reference genome , 2018, Science.

[47]  Matthew R. Tucker,et al.  Phenotypic and genetic analysis of spike and kernel characteristics in wheat reveals long-term genetic trends of grain yield components , 2018, Theoretical and Applied Genetics.

[48]  D. Villegas,et al.  Effect of Ppd-A1 and Ppd-B1 Allelic Variants on Grain Number and Thousand Kernel Weight of Durum Wheat and Their Impact on Final Grain Yield , 2018, Front. Plant Sci..

[49]  Yunfeng Xu,et al.  Genome-wide association and validation of key loci for yield-related traits in wheat founder parent Xiaoyan 6 , 2018, Molecular Breeding.

[50]  Jindong Liu,et al.  Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers , 2018, Theoretical and Applied Genetics.

[51]  Robert J. Schmitz,et al.  Zebularine treatment is associated with deletion of FT-B1 leading to an increase in spikelet number in bread wheat. , 2018, Plant, cell & environment.

[52]  A. Carter,et al.  Identification and validation of QTL for grain yield and plant water status under contrasting water treatments in fall-sown spring wheats , 2018, Theoretical and Applied Genetics.

[53]  M. Kabir,et al.  Global QTL Analysis Identifies Genomic Regions on Chromosomes 4A and 4B Harboring Stable Loci for Yield-Related Traits Across Different Environments in Wheat (Triticum aestivum L.) , 2018, Front. Plant Sci..

[54]  Liang Chen,et al.  Effects of Vrn-B1 and Ppd-D1 on developmental and agronomic traits in Rht5 dwarf plants of bread wheat , 2018 .

[55]  B. Steuernagel,et al.  Rht18 Semidwarfism in Wheat Is Due to Increased GA 2-oxidaseA9 Expression and Reduced GA Content1[OPEN] , 2018, Plant Physiology.

[56]  K. Siddique,et al.  The Effect of Grain Position on Genetic Improvement of Grain Number and Thousand Grain Weight in Winter Wheat in North China , 2018, Front. Plant Sci..

[57]  Yaxi Liu,et al.  Analysis of contributors to grain yield in wheat at the individual quantitative trait locus level , 2018 .

[58]  Q. Xue,et al.  Mapping of quantitative trait loci for grain yield and its components in a US popular winter wheat TAM 111 using 90K SNPs , 2017, PloS one.

[59]  P. Langridge,et al.  Early Flowering as a Drought Escape Mechanism in Plants: How Can It Aid Wheat Production? , 2017, Front. Plant Sci..

[60]  D. Thilmany,et al.  An Overview of Global Wheat Market Fundamentals in an Era of Climate Concerns , 2017 .

[61]  A. Rasheed,et al.  Genome-wide association study for agronomic and physiological traits in spring wheat evaluated in a range of heat prone environments , 2017, Theoretical and Applied Genetics.

[62]  Congwei Sun,et al.  Genome‐wide association study for 13 agronomic traits reveals distribution of superior alleles in bread wheat from the Yellow and Huai Valley of China , 2017, Plant biotechnology journal.

[63]  S. Dreisigacker,et al.  Genetic analysis of multi-environmental spring wheat trials identifies genomic regions for locus-specific trade-offs for grain weight and grain number , 2017, Theoretical and Applied Genetics.

[64]  Genlou Sun,et al.  Cloning and Characterization of TaTGW-7A Gene Associated with Grain Weight in Wheat via SLAF-seq-BSA , 2016, Front. Plant Sci..

[65]  D. Cui,et al.  A Single-Nucleotide Polymorphism of TaGS5 Gene Revealed its Association with Kernel Weight in Chinese Bread Wheat , 2015, Front. Plant Sci..

[66]  Jindong Liu,et al.  TaTGW6-A1, an ortholog of rice TGW6, is associated with grain weight and yield in bread wheat , 2015, Molecular Breeding.

[67]  Jindong Liu,et al.  Genome-Wide Linkage Mapping of QTL for Yield Components, Plant Height and Yield-Related Physiological Traits in the Chinese Wheat Cross Zhou 8425B/Chinese Spring , 2015, Front. Plant Sci..

[68]  P. Shewry,et al.  The contribution of wheat to human diet and health , 2015, Food and energy security.

[69]  T. Würschum,et al.  Multiply to conquer: Copy number variations at Ppd-B1 and Vrn-A1 facilitate global adaptation in wheat , 2015, BMC Genetics.

[70]  Kadambot H. M. Siddique,et al.  Wheat yield improvements in China: Past trends and future directions , 2015 .

[71]  Luyan Zhang,et al.  QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations , 2015 .

[72]  Zvi Peleg,et al.  Genetic evidence for differential selection of grain and embryo weight during wheat evolution under domestication , 2015, Journal of experimental botany.

[73]  Jindong Liu,et al.  TaTGW6-A1, an ortholog of rice TGW6, is associated with grain weight and yield in bread wheat , 2015, Molecular Breeding.

[74]  Zhikang Li,et al.  Genetic background effects on QTL and QTL × environment interaction for yield and its component traits as revealed by reciprocal introgression lines in rice , 2014 .

[75]  L. R. Nelson,et al.  ‘TAM 112’ Wheat, Resistant to Greenbug and Wheat Curl Mite and Adapted to the Dryland Production System in the Southern High Plains , 2014 .

[76]  Alison B. Smith,et al.  GrainScan: a low cost, fast method for grain size and colour measurements , 2014, Plant Methods.

[77]  Q. Xue,et al.  Molecular Markers Linked to Important Genes in Hard Winter Wheat , 2014 .

[78]  D. Bates,et al.  Fitting Linear Mixed-Effects Models Using lme4 , 2014, 1406.5823.

[79]  M. Ganal,et al.  Genetic architecture of main effect QTL for heading date in European winter wheat , 2014, Front. Plant Sci..

[80]  J. Dubcovsky,et al.  Characterization of FLOWERING LOCUS T1 (FT1) Gene in Brachypodium and Wheat , 2014, PloS one.

[81]  P. Langridge,et al.  Genetic control of grain yield and grain physical characteristics in a bread wheat population grown under a range of environmental conditions , 2014, Theoretical and Applied Genetics.

[82]  Qingwu Xue,et al.  Yield Determination and Water-Use Efficiency of Wheat under Water-Limited Conditions in the U.S. Southern High Plains , 2014 .

[83]  Ying Guo,et al.  Haplotype, molecular marker and phenotype effects associated with mineral nutrient and grain size traits of TaGS1a in wheat , 2013 .

[84]  R. E. Mason,et al.  QTL for yield, yield components and canopy temperature depression in wheat under late sown field conditions , 2013, Euphytica.

[85]  Trevor W. Rife,et al.  Genotyping‐by‐Sequencing for Plant Breeding and Genetics , 2012 .

[86]  G. Horn,et al.  'Duster' wheat: A durable, dual-purpose cultivar adapted to the southern great plains of the USA , 2012 .

[87]  J. Jia,et al.  Discovery, evaluation and distribution of haplotypes of the wheat Ppd-D1 gene. , 2010, The New phytologist.

[88]  Chenyang Hao,et al.  Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.) , 2010, Theoretical and Applied Genetics.

[89]  R. Trethowan,et al.  Novel Germplasm Resources for Improving Environmental Stress Tolerance of Hexaploid Wheat , 2008 .

[90]  Ann Lehman,et al.  JMP start statistics : a guide to statistics and data analysis using JMP , 2012 .

[91]  D. Mackill,et al.  Marker-assisted selection: an approach for precision plant breeding in the twenty-first century , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

[92]  Edward S. Buckler,et al.  TASSEL: software for association mapping of complex traits in diverse samples , 2007, Bioinform..

[93]  P. Langridge,et al.  Genetic dissection of grain yield in bread wheat. I. QTL analysis , 2007, Theoretical and Applied Genetics.

[94]  P. Langridge,et al.  Genetic dissection of grain yield in bread wheat. II. QTL-by-environment interaction , 2007, Theoretical and Applied Genetics.

[95]  J. Kyozuka,et al.  Rice ABERRANT PANICLE ORGANIZATION 1, encoding an F-box protein, regulates meristem fate. , 2007, The Plant journal : for cell and molecular biology.

[96]  D. Laurie,et al.  A Pseudo-Response Regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.) , 2007, Theoretical and Applied Genetics.

[97]  Xinhua Zhao,et al.  A intervarietal genetic map and QTL analysis for yield traits in wheat , 2007, Molecular Breeding.

[98]  L. Yan,et al.  The wheat and barley vernalization gene VRN3 is an orthologue of FT , 2006, Proceedings of the National Academy of Sciences.

[99]  J. Ooijen,et al.  JoinMap® 4, Software for the calculation of genetic linkage maps in experimental populations , 2006 .

[100]  G. Wenzel,et al.  Genetic and physical mapping of photoperiod insensitive gene Ppd-B1 in common wheat , 2004, Euphytica.

[101]  Peter Hedden,et al.  The genes of the Green Revolution. , 2003, Trends in genetics : TIG.

[102]  F. Salamini,et al.  Catalogue of gene symbols for wheat , 1998 .

[103]  G. Slafer,et al.  Genetic improvement in wheat yield and associated traits. A re‐examination of previous results and the latest trends , 1995 .

[104]  R. Allan.  Agronomic Comparisons Between Rht1 and Rht2 Semidwarf Genes in Winter Wheat , 1989 .

[105]  D. D. Kosambi.  The estimation of map distances from recombination values. , 1943 .