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Ding Y, Fang H, Gao Y, Fan G, Shi X, Yu S, Ding S, Huang T, Wang W, Song J. Genome-wide association analysis of time to heading and maturity in bread wheat using 55K microarrays. FRONTIERS IN PLANT SCIENCE 2023; 14:1296197. [PMID: 38107003 PMCID: PMC10722194 DOI: 10.3389/fpls.2023.1296197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023]
Abstract
To investigate the genetic mechanisms underlying the reproductive traits (time to flowering and maturity) in wheat and identify candidate genes associated, a phenotypic analysis was conducted on 239 wheat accessions (lines) from around the world. A genome-wide association study (GWAS) of wheat heading and maturity phases was performed using the MLM (Q+K) model in the TASSLE software, combined with the Wheat 55K SNP array. The results revealed significant phenotypic variation in heading and maturity among the wheat accessions across different years, with coefficients of variation ranging from 0.96% to 1.97%. The phenotypic data from different years exhibited excellent correlation, with a genome-wide linkage disequilibrium (LD) attenuation distance of 3 Mb. Population structure analysis, evolutionary tree analysis, and principal component analysis indicated that the 239 wheat accessions formed a relatively homogeneous natural population, which could be divided into three subgroups. The GWAS results identified a total of 293 SNP marker loci that were significantly associated with wheat heading and maturity stages (P ≤ 0.001) in different environments. Among them, nine stable SNP marker loci were consistently detected in multiple environments. These marker loci were distributed on wheat chromosomes 1A、1B、2D、3A、5B、6D and 7A. Each individual locus explained 4.03%-16.06% of the phenotypic variation. Furthermore, through careful analysis of the associated loci with large phenotypic effect values and stable inheritance, a total of nine candidate genes related to wheat heading and maturity stages were identified. These findings have implications for molecular marker-assisted selection breeding programs targeting specific wheat traits at the heading and maturity stages. In summary, this study conducted a comprehensive GWAS of wheat heading and maturity phases, revealing significant associations between genetic markers and key developmental stages in wheat. The identification of candidate genes and marker loci provides valuable information for further studies on wheat breeding and genetic improvement targeted at enhancing heading and maturity traits.
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Affiliation(s)
- Yindeng Ding
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Hui Fang
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Yonghong Gao
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Guiqiang Fan
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Xiaolei Shi
- Institute of Crop Variety Resources, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Shan Yu
- College of Agriculture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Sunlei Ding
- Institute of Crop Variety Resources, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Tianrong Huang
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Wei Wang
- Department of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang, China
| | - Jikun Song
- Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
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Berraies S, Cuthbert R, Knox R, Singh A, DePauw R, Ruan Y, Bokore F, Henriquez MA, Kumar S, Burt A, Pozniak C, N’Diaye A, Meyer B. High-density genetic mapping of Fusarium head blight resistance and agronomic traits in spring wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1134132. [PMID: 37284725 PMCID: PMC10241073 DOI: 10.3389/fpls.2023.1134132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/03/2023] [Indexed: 06/08/2023]
Abstract
Fusarium head blight (FHB) has rapidly become a major challenge to successful wheat production and competitive end-use quality in western Canada. Continuous effort is required to develop germplasm with improved FHB resistance and understand how to incorporate the material into crossing schemes for marker-assisted selection and genomic selection. The aim of this study was to map quantitative trait loci (QTL) responsible for the expression of FHB resistance in two adapted cultivars and to evaluate their co-localization with plant height, days to maturity, days to heading, and awnedness. A large doubled haploid population of 775 lines developed from cultivars Carberry and AC Cadillac was assessed for FHB incidence and severity in nurseries near Portage la Prairie, Brandon, and Morden in different years, and for plant height, awnedness, days to heading, and days to maturity near Swift Current. An initial linkage map using a subset of 261 lines was constructed using 634 polymorphic DArT and SSR markers. QTL analysis revealed five resistance QTL on chromosomes 2A, 3B (two loci), 4B, and 5A. A second genetic map with increased marker density was constructed using the Infinium iSelect 90k SNP wheat array in addition to the previous DArT and SSR markers, which revealed two additional QTL on 6A and 6D. The complete population was genotyped, and a total of 6,806 Infinium iSelect 90k SNP polymorphic markers were used to identify 17 putative resistance QTL on 14 different chromosomes. As with the smaller population size and fewer markers, large-effect QTL were detected on 3B, 4B, and 5A that were consistently expressed across environments. FHB resistance QTL were co-localized with plant height QTL on chromosomes 4B, 6D, and 7D; days to heading on 2B, 3A, 4A, 4B, and 5A; and maturity on 3A, 4B, and 7D. A major QTL for awnedness was identified as being associated with FHB resistance on chromosome 5A. Nine small-effect QTL were not associated with any of the agronomic traits, whereas 13 QTL that were associated with agronomic traits did not co-localize with any of the FHB traits. There is an opportunity to select for improved FHB resistance within adapted cultivars by using markers associated with complementary QTL.
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Affiliation(s)
- Samia Berraies
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Richard Cuthbert
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Ron Knox
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | | | - Yuefeng Ruan
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Firdissa Bokore
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Santosh Kumar
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Andrew Burt
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Amidou N’Diaye
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brad Meyer
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
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Dhakal S, Liu X, Chu C, Yang Y, Rudd JC, Ibrahim AMH, Xue Q, Devkota RN, Baker JA, Baker SA, Simoneaux BE, Opena GB, Sutton R, Jessup KE, Hui K, Wang S, Johnson CD, Metz RP, Liu S. Genome-wide QTL mapping of yield and agronomic traits in two widely adapted winter wheat cultivars from multiple mega-environments. PeerJ 2021; 9:e12350. [PMID: 34900409 PMCID: PMC8627123 DOI: 10.7717/peerj.12350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/29/2021] [Indexed: 12/01/2022] Open
Abstract
Quantitative trait loci (QTL) analysis could help to identify suitable molecular markers for marker-assisted breeding (MAB). A mapping population of 124 F5:7recombinant inbred lines derived from the cross ‘TAM 112’/‘TAM 111’ was grown under 28 diverse environments and evaluated for grain yield, test weight, heading date, and plant height. The objective of this study was to detect QTL conferring grain yield and agronomic traits from multiple mega-environments. Through a linkage map with 5,948 single nucleotide polymorphisms (SNPs), 51 QTL were consistently identified in two or more environments or analyses. Ten QTL linked to two or more traits were also identified on chromosomes 1A, 1D, 4B, 4D, 6A, 7B, and 7D. Those QTL explained up to 13.3% of additive phenotypic variations with the additive logarithm of odds (LOD(A)) scores up to 11.2. The additive effect increased yield up to 8.16 and 6.57 g m−2 and increased test weight by 2.14 and 3.47 kg m−3 with favorable alleles from TAM 111 and TAM 112, respectively. Seven major QTL for yield and six for TW with one in common were of our interest on MAB as they explained 5% or more phenotypic variations through additive effects. This study confirmed previously identified loci and identified new QTL and the favorable alleles for improving grain yield and agronomic traits.
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Affiliation(s)
- Smit Dhakal
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Xiaoxiao Liu
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Chenggen Chu
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America.,Edward T. Schafer Agricultural Research Center, Sugarbeet & Potato Research Unit, USDA-ARS, Fargo, ND, United States of America
| | - Yan Yang
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Jackie C Rudd
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Amir M H Ibrahim
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States of America
| | - Qingwu Xue
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Ravindra N Devkota
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Jason A Baker
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Shannon A Baker
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Bryan E Simoneaux
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States of America
| | - Geraldine B Opena
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States of America
| | - Russell Sutton
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States of America
| | - Kirk E Jessup
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Kele Hui
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Shichen Wang
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX, United States of America
| | - Charles D Johnson
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX, United States of America
| | - Richard P Metz
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX, United States of America
| | - Shuyu Liu
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
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4
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Han R, Lavelle D, Truco MJ, Michelmore R. Quantitative Trait Loci and Candidate Genes Associated with Photoperiod Sensitivity in Lettuce (Lactuca spp.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3473-3487. [PMID: 34245320 PMCID: PMC8440299 DOI: 10.1007/s00122-021-03908-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE A population of lettuce that segregated for photoperiod sensitivity was planted under long-day and short-day conditions. Genetic mapping revealed two distinct sets of QTLs controlling daylength-independent and photoperiod-sensitive flowering time. The molecular mechanism of flowering time regulation in lettuce is of interest to both geneticists and breeders because of the extensive impact of this trait on agricultural production. Lettuce is a facultative long-day plant which changes in flowering time in response to photoperiod. Variations exist in both flowering time and the degree of photoperiod sensitivity among accessions of wild (Lactuca serriola) and cultivated (L. sativa) lettuce. An F6 population of 236 recombinant inbred lines (RILs) was previously developed from a cross between a late-flowering, photoperiod-sensitive L. serriola accession and an early-flowering, photoperiod-insensitive L. sativa accession. This population was planted under long-day (LD) and short-day (SD) conditions in a total of four field and screenhouse trials; the developmental phenotype was scored weekly in each trial. Using genotyping-by-sequencing (GBS) data of the RILs, quantitative trait loci (QTL) mapping revealed five flowering time QTLs that together explained more than 20% of the variation in flowering time under LD conditions. Using two independent statistical models to extract the photoperiod sensitivity phenotype from the LD and SD flowering time data, we identified an additional five QTLs that together explained more than 30% of the variation in photoperiod sensitivity in the population. Orthology and sequence analysis of genes within the nine QTLs revealed potential functional equivalents in the lettuce genome to the key regulators of flowering time and photoperiodism, FD and CONSTANS, respectively, in Arabidopsis.
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Affiliation(s)
- Rongkui Han
- The Plant Biology Graduate Group, University of California, Davis, 95616, USA
- The Genome Center, University of California, Davis, 95616, USA
| | - Dean Lavelle
- The Genome Center, University of California, Davis, 95616, USA
| | | | - Richard Michelmore
- The Genome Center, University of California, Davis, 95616, USA.
- Department of Plant Sciences, University of California, Davis, 95616, USA.
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5
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Rabbi SMHA, Kumar A, Mohajeri Naraghi S, Sapkota S, Alamri MS, Elias EM, Kianian S, Seetan R, Missaoui A, Solanki S, Mergoum M. Identification of Main-Effect and Environmental Interaction QTL and Their Candidate Genes for Drought Tolerance in a Wheat RIL Population Between Two Elite Spring Cultivars. Front Genet 2021; 12:656037. [PMID: 34220939 PMCID: PMC8249774 DOI: 10.3389/fgene.2021.656037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/13/2021] [Indexed: 01/22/2023] Open
Abstract
Understanding the genetics of drought tolerance can expedite the development of drought-tolerant cultivars in wheat. In this study, we dissected the genetics of drought tolerance in spring wheat using a recombinant inbred line (RIL) population derived from a cross between a drought-tolerant cultivar, ‘Reeder’ (PI613586), and a high-yielding but drought-susceptible cultivar, ‘Albany.’ The RIL population was evaluated for grain yield (YLD), grain volume weight (GVW), thousand kernel weight (TKW), plant height (PH), and days to heading (DH) at nine different environments. The Infinium 90 k-based high-density genetic map was generated using 10,657 polymorphic SNP markers representing 2,057 unique loci. Quantitative trait loci (QTL) analysis detected a total of 11 consistent QTL for drought tolerance-related traits. Of these, six QTL were exclusively identified in drought-prone environments, and five were constitutive QTL (identified under both drought and normal conditions). One major QTL on chromosome 7B was identified exclusively under drought environments and explained 13.6% of the phenotypic variation (PV) for YLD. Two other major QTL were detected, one each on chromosomes 7B and 2B under drought-prone environments, and explained 14.86 and 13.94% of phenotypic variation for GVW and YLD, respectively. One novel QTL for drought tolerance was identified on chromosome 2D. In silico expression analysis of candidate genes underlaying the exclusive QTLs associated with drought stress identified the enrichment of ribosomal and chloroplast photosynthesis-associated proteins showing the most expression variability, thus possibly contributing to stress response by modulating the glycosyltransferase (TraesCS6A01G116400) and hexosyltransferase (TraesCS7B01G013300) unique genes present in QTL 21 and 24, respectively. While both parents contributed favorable alleles to these QTL, unexpectedly, the high-yielding and less drought-tolerant parent contributed desirable alleles for drought tolerance at four out of six loci. Regardless of the origin, all QTL with significant drought tolerance could assist significantly in the development of drought-tolerant wheat cultivars, using genomics-assisted breeding approaches.
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Affiliation(s)
- S M Hisam Al Rabbi
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | | | - Suraj Sapkota
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States
| | - Mohammed S Alamri
- Department of Food Science and Nutrition, King Saud University, Riyadh, Saudi Arabia
| | - Elias M Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Shahryar Kianian
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, United States
| | - Raed Seetan
- Department of Computer Science, Slippery Rock University, Slippery Rock, PA, United States
| | - Ali Missaoui
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
| | - Shyam Solanki
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Mohamed Mergoum
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
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Vitale P, Fania F, Esposito S, Pecorella I, Pecchioni N, Palombieri S, Sestili F, Lafiandra D, Taranto F, De Vita P. QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents. Genes (Basel) 2021; 12:genes12040604. [PMID: 33923933 PMCID: PMC8074140 DOI: 10.3390/genes12040604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 01/20/2023] Open
Abstract
Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F2 and F2-derived F3 families) and late (F6 and F7, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F2 and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F2 mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.
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Affiliation(s)
- Paolo Vitale
- Department of Agriculture, Food, Natural Science, Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (P.V.); (F.F.)
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Fabio Fania
- Department of Agriculture, Food, Natural Science, Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (P.V.); (F.F.)
| | - Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Ivano Pecorella
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Samuela Palombieri
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (S.P.); (F.S.); (D.L.)
| | - Francesco Sestili
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (S.P.); (F.S.); (D.L.)
| | - Domenico Lafiandra
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (S.P.); (F.S.); (D.L.)
| | - Francesca Taranto
- Institute of Biosciences and Bioresources (CNR-IBBR), 80055 Portici, Italy
- Correspondence: (F.T.); (P.D.V.)
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
- Correspondence: (F.T.); (P.D.V.)
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7
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Bogard M, Hourcade D, Piquemal B, Gouache D, Deswartes JC, Throude M, Cohan JP. Marker-based crop model-assisted ideotype design to improve avoidance of abiotic stress in bread wheat. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1085-1103. [PMID: 33068400 DOI: 10.1093/jxb/eraa477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/12/2020] [Indexed: 05/22/2023]
Abstract
Wheat phenology allows escape from seasonal abiotic stresses including frosts and high temperatures, the latter being forecast to increase with climate change. The use of marker-based crop models to identify ideotypes has been proposed to select genotypes adapted to specific weather and management conditions and anticipate climate change. In this study, a marker-based crop model for wheat phenology was calibrated and tested. Climate analysis of 30 years of historical weather data in 72 locations representing the main wheat production areas in France was performed. We carried out marker-based crop model simulations for 1019 wheat cultivars and three sowing dates, which allowed calculation of genotypic stress avoidance frequencies of frost and heat stress and identification of ideotypes. The phenology marker-based crop model allowed prediction of large genotypic variations for the beginning of stem elongation (GS30) and heading date (GS55). Prediction accuracy was assessed using untested genotypes and environments, and showed median genotype prediction errors of 8.5 and 4.2 days for GS30 and GS55, respectively. Climate analysis allowed the definition of a low risk period for each location based on the distribution of the last frost and first heat days. Clustering of locations showed three groups with contrasting levels of frost and heat risks. Marker-based crop model simulations showed the need to optimize the genotype depending on sowing date, particularly in high risk environments. An empirical validation of the approach showed that it holds good promises to improve frost and heat stress avoidance.
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Affiliation(s)
- Matthieu Bogard
- Arvalis - Institut du Végétal, 6 Chemin de la côte vieille, Baziège, France
| | - Delphine Hourcade
- Arvalis - Institut du Végétal, 6 Chemin de la côte vieille, Baziège, France
| | - Benoit Piquemal
- Arvalis - Institut du Végétal, station expérimentale, Boigneville, France
| | | | - Jean-Charles Deswartes
- Arvalis - Institut du Végétal, Route de Châteaufort ZA des graviers, Villiers-le-Bâcle, France
| | - Mickael Throude
- Biogemma: Centre de Recherche de Chappes, Route d'Ennezat, CS, Chappes, France
| | - Jean-Pierre Cohan
- Arvalis - Institut du Végétal, Station expérimentale de La Jaillière, La Chapelle Saint-Sauveur, Loireauxence, France
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8
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Bao B, Chao H, Wang H, Zhao W, Zhang L, Raboanatahiry N, Wang X, Wang B, Jia H, Li M. Stable, Environmental Specific and Novel QTL Identification as Well as Genetic Dissection of Fatty Acid Metabolism in Brassica napus. FRONTIERS IN PLANT SCIENCE 2018; 9:1018. [PMID: 30065738 PMCID: PMC6057442 DOI: 10.3389/fpls.2018.01018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/22/2018] [Indexed: 05/05/2023]
Abstract
Fatty acid (FA) composition is the typical quantitative trait in oil seed crops, of which study is not only closely related to oil content, but is also more critical for the quality improvement of seed oil. The double haploid (DH) population named KN with a high density SNP linkage map was applied for quantitative trait loci (QTL) analysis of FA composition in this study. A total of 406 identified QTL were detected for eight FA components with an average confidence interval (CI) of 2.92 cM, the explained phenotypic variation (PV) value ranged from 1.49 to 45.05%. Totally, 204 consensus and 91 unique QTL were further obtained via meta-analysis method for the purpose of detecting multiple environment expressed and pleiotropic QTL, respectively. Of which, 74 stable expressed and 22 environmental specific QTL were also revealed, respectively. In order to make clear the genetic mechanism of FA metabolism at individual QTL level, conditional QTL analysis was also conducted and more than two thousand conditional QTL which could not be detected under the unconditional mapping were detected, which indicated the complex interrelationship of the QTL controlling FA content in rapeseed. Through comparative genomic analysis and homologous gene annotation, 61 candidates related to acyl lipid metabolism were identified underlying the CI of FA QTL. To further visualize the genetic mechanism of FA metabolism, an intuitive and meticulous network about acyl lipid metabolism was constructed and some closely related candidates were positioned. This study provided a more accurate localization for stable and pleiotropic QTL, and a deeper dissection of the molecular regulatory mechanism of FA metabolism in rapeseed.
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Affiliation(s)
- Binghao Bao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Chao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China
| | - Weiguo Zhao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China
| | - Lina Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Nadia Raboanatahiry
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaodong Wang
- Provincial Key Laboratory of Agrobiology, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Baoshan Wang
- College of Life Science, Shandong Normal University, Jinan, China
| | - Haibo Jia
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Haibo Jia
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
- Maoteng Li
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9
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Luo W, Ma J, Zhou XH, Sun M, Kong XC, Wei YM, Jiang YF, Qi PF, Jiang QT, Liu YX, Peng YY, Chen GY, Zheng YL, Liu C, Lan XJ. Identification of Quantitative Trait Loci Controlling Agronomic Traits Indicates Breeding Potential of Tibetan Semiwild Wheat ( Triticum aestivum
ssp. tibetanum
). CROP SCIENCE 2016. [PMID: 0 DOI: 10.2135/cropsci2015.11.0700] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- Wei Luo
- Triticeae Research Institute; Sichuan Agricultural Univ.; 211 Huimin Road Wenjiang, Chengdu Sichuan 611130 China
| | - Jian Ma
- Triticeae Research Institute; Sichuan Agricultural Univ.; 211 Huimin Road Wenjiang, Chengdu Sichuan 611130 China
| | - Xiao-Hong Zhou
- Triticeae Research Institute; Sichuan Agricultural Univ.; 211 Huimin Road Wenjiang, Chengdu Sichuan 611130 China
| | - Min Sun
- Triticeae Research Institute; Sichuan Agricultural Univ.; 211 Huimin Road Wenjiang, Chengdu Sichuan 611130 China
| | - Xing-Chen Kong
- Triticeae Research Institute; Sichuan Agricultural Univ.; 211 Huimin Road Wenjiang, Chengdu Sichuan 611130 China
| | - Yu-Ming Wei
- Triticeae Research Institute; Sichuan Agricultural Univ.; 211 Huimin Road Wenjiang, Chengdu Sichuan 611130 China
| | - Yun-Feng Jiang
- Triticeae Research Institute; Sichuan Agricultural Univ.; 211 Huimin Road Wenjiang, Chengdu Sichuan 611130 China
| | - Peng-Fei Qi
- Triticeae Research Institute; Sichuan Agricultural Univ.; 211 Huimin Road Wenjiang, Chengdu Sichuan 611130 China
| | - Qian-Tao Jiang
- Triticeae Research Institute; Sichuan Agricultural Univ.; 211 Huimin Road Wenjiang, Chengdu Sichuan 611130 China
| | - Ya-Xi Liu
- Triticeae Research Institute; Sichuan Agricultural Univ.; 211 Huimin Road Wenjiang, Chengdu Sichuan 611130 China
| | - Yuan-Ying Peng
- Triticeae Research Institute; Sichuan Agricultural Univ.; 211 Huimin Road Wenjiang, Chengdu Sichuan 611130 China
| | - Guo-Yue Chen
- Triticeae Research Institute; Sichuan Agricultural Univ.; 211 Huimin Road Wenjiang, Chengdu Sichuan 611130 China
| | - You-Liang Zheng
- Key Laboratory of Southwestern Crop Germplasm Utilization; Ministry of Agriculture; Sichuan Agricultural Univ.; 211 Huimin Road Wenjiang, Chengdu Sichuan 611130
| | - Chunji Liu
- CSIRO Agriculture Flagship; 306 Carmody Road St Lucia QLD 4067
- Australia and School of Plant Biology; Univ. of Western Australia; Perth WA 6009 Australia
| | - Xiu-Jin Lan
- Triticeae Research Institute; Sichuan Agricultural Univ.; 211 Huimin Road Wenjiang, Chengdu Sichuan 611130 China
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10
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Bogard M, Ravel C, Paux E, Bordes J, Balfourier F, Chapman SC, Le Gouis J, Allard V. Predictions of heading date in bread wheat (Triticum aestivum L.) using QTL-based parameters of an ecophysiological model. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5849-65. [PMID: 25148833 PMCID: PMC4203124 DOI: 10.1093/jxb/eru328] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Prediction of wheat phenology facilitates the selection of cultivars with specific adaptations to a particular environment. However, while QTL analysis for heading date can identify major genes controlling phenology, the results are limited to the environments and genotypes tested. Moreover, while ecophysiological models allow accurate predictions in new environments, they may require substantial phenotypic data to parameterize each genotype. Also, the model parameters are rarely related to all underlying genes, and all the possible allelic combinations that could be obtained by breeding cannot be tested with models. In this study, a QTL-based model is proposed to predict heading date in bread wheat (Triticum aestivum L.). Two parameters of an ecophysiological model (V sat and P base , representing genotype vernalization requirements and photoperiod sensitivity, respectively) were optimized for 210 genotypes grown in 10 contrasting location × sowing date combinations. Multiple linear regression models predicting V sat and P base with 11 and 12 associated genetic markers accounted for 71 and 68% of the variance of these parameters, respectively. QTL-based V sat and P base estimates were able to predict heading date of an independent validation data set (88 genotypes in six location × sowing date combinations) with a root mean square error of prediction of 5 to 8.6 days, explaining 48 to 63% of the variation for heading date. The QTL-based model proposed in this study may be used for agronomic purposes and to assist breeders in suggesting locally adapted ideotypes for wheat phenology.
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Affiliation(s)
- Matthieu Bogard
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - Catherine Ravel
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - Etienne Paux
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - Jacques Bordes
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - François Balfourier
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - Scott C Chapman
- CSIRO, Queensland Bioscience Precinct - St Lucia, 306 Carmody Road, St Lucia QLD 4067, Australia
| | - Jacques Le Gouis
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - Vincent Allard
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
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11
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Conditional and unconditional QTL mapping of drought-tolerance-related traits of wheat seedling using two related RIL populations. J Genet 2014; 92:213-31. [PMID: 23970077 DOI: 10.1007/s12041-013-0253-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
For discovering the quantitative trait loci (QTLs) contributing to early seedling growth and drought tolerance during germination, conditional and unconditional analyses of 12 traits of wheat seedlings: coleoptile length, seedling height, longest root length, root number, seedling fresh weight, stem and leaves fresh weight, root fresh weight, seedling dry weight, stem and leaves dry weight, root dry weight, root to shoot fresh weight ratio, root-to-shoot dry weight ratio, were conducted under two water conditions using two F8:9 recombinant inbred line (RIL) populations. The results of unconditional analysis are as follows: 88 QTLs accounting for 3.33-77.01% of the phenotypic variations were detected on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5A, 5B, 5D, 6A, 6B, 6D, 7A, 7B and 7D. Among these QTLs, 19 were main-effect QTLs with a contribution rate greater than 10%. The results of the conditional QTL analysis of 12 traits under osmotic stress on normal water conditions were as follows: altogether 22 QTLs concerned with drought tolerance were detected on chromosomes 1B, 2A, 2B, 3B, 4A, 5D, 6A, 6D, 7B, and 7D. Of these QTLs, six were main-effect QTLs. These 22 QTLs were all special loci directly concerned with drought tolerance and most of them could not be detected by unconditional analysis. The finding of these QTLs has an important significance for fine-mapping technique, map-based cloning, and molecular marker-assisted selection of early seedling traits, such as growth and drought tolerance.
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12
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Allele Variation in Loci for Adaptive Response and Plant Height and its Effect on Grain Yield in Wheat. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.2478/v10133-010-0042-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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13
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Zanke C, Ling J, Plieske J, Kollers S, Ebmeyer E, Korzun V, Argillier O, Stiewe G, Hinze M, Beier S, Ganal MW, Röder MS. Genetic architecture of main effect QTL for heading date in European winter wheat. FRONTIERS IN PLANT SCIENCE 2014; 5:217. [PMID: 24904613 PMCID: PMC4033046 DOI: 10.3389/fpls.2014.00217] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 05/01/2014] [Indexed: 05/20/2023]
Abstract
A genome-wide association study (GWAS) for heading date (HD) was performed with a panel of 358 European winter wheat (Triticum aestivum L.) varieties and 14 spring wheat varieties through the phenotypic evaluation of HD in field tests in eight environments. Genotyping data consisted of 770 mapped microsatellite loci and 7934 mapped SNP markers derived from the 90K iSelect wheat chip. Best linear unbiased estimations (BLUEs) were calculated across all trials and ranged from 142.5 to 159.6 days after the 1st of January with an average value of 151.4 days. Considering only associations with a -log10 (P-value) ≥ 3.0, a total of 340 SSR and 2983 SNP marker-trait associations (MTAs) were detected. After Bonferroni correction for multiple testing, a total of 72 SSR and 438 SNP marker-trait associations remained significant. Highly significant MTAs were detected for the photoperiodism gene Ppd-D1, which was genotyped in all varieties. Consistent associations were found on all chromosomes with the highest number of MTAs on chromosome 5B. Linear regression showed a clear dependence of the HD score BLUEs on the number of favorable alleles (decreasing HD) and unfavorable alleles (increasing HD) per variety meaning that genotypes with a higher number of favorable or a low number of unfavorable alleles showed lower HD and therefore flowered earlier. For the vernalization gene Vrn-A2 co-locating MTAs on chromosome 5A, as well as for the photoperiodism genes Ppd-A1 and Ppd-B1 on chromosomes 2A and 2B were detected. After the construction of an integrated map of the SSR and SNP markers and by exploiting the synteny to sequenced species, such as rice and Brachypodium distachyon, we were able to demonstrate that a marker locus on wheat chromosome 5BL with homology to the rice photoperiodism gene Hd6 played a significant role in the determination of the heading date in wheat.
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Affiliation(s)
- Christine Zanke
- Department of Cytogenetics and Genome Analyses, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Jie Ling
- Department of Cytogenetics and Genome Analyses, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | | | | | | | | | | | | | | | - Sebastian Beier
- Department of Cytogenetics and Genome Analyses, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | | | - Marion S. Röder
- Department of Cytogenetics and Genome Analyses, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
- *Correspondence: Marion S. Röder, Department of Cytogenetics and Genome Analyses, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben 06466, Germany e-mail:
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14
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Milec Z, Valárik M, Bartoš J, Šafář J. Can a late bloomer become an early bird? Tools for flowering time adjustment. Biotechnol Adv 2014; 32:200-14. [DOI: 10.1016/j.biotechadv.2013.09.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/23/2013] [Accepted: 09/24/2013] [Indexed: 11/25/2022]
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15
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Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl Acad Sci U S A 2013; 110:8057-62. [PMID: 23630259 DOI: 10.1073/pnas.1217133110] [Citation(s) in RCA: 574] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject to selection during improvement, we developed a high-throughput array to interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. Using a SNP-based diversity map we characterized the impact of crop improvement on genomic and geographic patterns of genetic diversity. We found evidence of a small population bottleneck and extensive use of ancestral variation often traceable to founders of cultivars from diverse geographic regions. Analyzing genetic differentiation among populations and the extent of haplotype sharing, we identified allelic variants subjected to selection during improvement. Selective sweeps were found around genes involved in the regulation of flowering time and phenology. An introgression of a wild relative-derived gene conferring resistance to a fungal pathogen was detected by haplotype-based analysis. Comparing selective sweeps identified in different populations, we show that selection likely acts on distinct targets or multiple functionally equivalent alleles in different portions of the geographic range of wheat. The majority of the selected alleles were present at low frequency in local populations, suggesting either weak selection pressure or temporal variation in the targets of directional selection during breeding probably associated with changing agricultural practices or environmental conditions. The developed SNP chip and map of genetic variation provide a resource for advancing wheat breeding and supporting future population genomic and genome-wide association studies in wheat.
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16
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Buerstmayr M, Huber K, Heckmann J, Steiner B, Nelson JC, Buerstmayr H. Mapping of QTL for Fusarium head blight resistance and morphological and developmental traits in three backcross populations derived from Triticum dicoccum × Triticum durum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1751-65. [PMID: 22926291 PMCID: PMC3493669 DOI: 10.1007/s00122-012-1951-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 07/15/2012] [Indexed: 05/21/2023]
Abstract
Breeding for resistance to Fusarium head blight (FHB) in durum wheat continues to be hindered by the lack of effective resistance sources. Only limited information is available on resistance QTL for FHB in tetraploid wheat. In this study, resistance to FHB of a Triticum dicoccum line in the background of three Austrian T. durum cultivars was genetically characterized. Three populations of BC(1)F(4)-derived RILs were developed from crosses between the resistant donor line T. dicoccum-161 and the Austrian T. durum recipient varieties DS-131621, Floradur and Helidur. About 130 BC(1)F(4)-derived lines per population were evaluated for FHB response using artificial spray inoculation in four field experiments during two seasons. Lines were genetically fingerprinted using SSR and AFLP markers. Genomic regions on chromosomes 3B, 4B, 6A, 6B and 7B were significantly associated with FHB severity. FHB resistance QTL on 6B and 7B were identified in two populations and a resistance QTL on 4B appeared in three populations. The alleles that enhanced FHB resistance were derived from the T. dicoccum parent, except for the QTL on chromosome 3B. All QTL except the QTL on 6A mapped to genomic regions where QTL for FHB have previously been reported in hexaploid wheat. QTL on 3B and 6B coincided with Fhb1 and Fhb2, respectively. This implies that tetraploid and hexaploid wheat share common genomic regions associated with FHB resistance. QTL for FHB resistance on 4B co-located with a major QTL for plant height and mapped at the position of the Rht-B1 gene, while QTL on 7B overlapped with QTL for flowering time.
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Affiliation(s)
- Maria Buerstmayr
- Department for Agrobiotechnology Tulln, BOKU-University of Natural Resources and Life Sciences-Vienna, Konrad Lorenz Str. 20, 3430 Tulln, Austria
| | - Karin Huber
- Department for Agrobiotechnology Tulln, BOKU-University of Natural Resources and Life Sciences-Vienna, Konrad Lorenz Str. 20, 3430 Tulln, Austria
- Present Address: Presse und Informationsdienst Agrarisches Informationszentrum (AIZ), Schauflergasse 6, 1014 Vienna, Austria
| | - Johannes Heckmann
- Department for Agrobiotechnology Tulln, BOKU-University of Natural Resources and Life Sciences-Vienna, Konrad Lorenz Str. 20, 3430 Tulln, Austria
- Present Address: Rijk Zwaan Nederland B.V., Burgemeester Crezéelaan, P.O. Box 40, 2678 ZG De Lier, The Netherlands
| | - Barbara Steiner
- Department for Agrobiotechnology Tulln, BOKU-University of Natural Resources and Life Sciences-Vienna, Konrad Lorenz Str. 20, 3430 Tulln, Austria
| | - James C. Nelson
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Hermann Buerstmayr
- Department for Agrobiotechnology Tulln, BOKU-University of Natural Resources and Life Sciences-Vienna, Konrad Lorenz Str. 20, 3430 Tulln, Austria
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17
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Takenaka S, Kawahara T. Evolution and dispersal of emmer wheat (Triticum sp.) from novel haplotypes of Ppd-1 (photoperiod response) genes and their surrounding DNA sequences. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:999-1014. [PMID: 22639190 DOI: 10.1007/s00122-012-1890-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 04/27/2012] [Indexed: 06/01/2023]
Abstract
The sequence data from 5' UTR, intronic, coding and 3' UTR regions of Ppd-A1 and Ppd-B1 were investigated for a total of 158 accessions of emmer wheat landraces comprising 19 of wild emmer wheat (Triticum dicoccoides), 45 of hulled emmer wheat (T. dicoccum) and 94 of free-threshing (FT) emmer wheat (T. durum etc.). We detected some novel types of deletions in the coding regions from 22 hulled emmer accessions and 20 FT emmer accessions. Emmer wheat accessions with these deletions could produce predicted proteins likely to lack function. We also observed some novel mutations in Ppd-B1. Sixty-seven and forty-one haplotypes were found in Ppd-A1 and Ppd-B1, respectively. Some mutations found in this study have not been known, so they have potential for useful genetic resources for wheat breeding. On the basis of sequence data from the 5' UTR region, both Ppd-A1 and Ppd-B1 haplotypes were divided into two groups (Type AI/AII and Type BI/BII). Types AI and AII of Ppd-A1 suggested gene flow between wild and hulled emmer. On the other hand, Types BI and BII of Ppd-B1 suggested gene flow between wild and FT emmer. More than half of hulled emmer accessions were Type AII/BI but few FT emmer accessions were of this type. Therefore, over half of the hulled emmer did not contribute to evolution of FT emmer.
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Affiliation(s)
- Shotaro Takenaka
- Laboratory of Crop Evolution, Plant Germ-plasm Institute, Graduate School of Agriculture, Kyoto University, Muko, Kyoto 617-0001, Japan.
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18
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Díaz A, Zikhali M, Turner AS, Isaac P, Laurie DA. Copy number variation affecting the Photoperiod-B1 and Vernalization-A1 genes is associated with altered flowering time in wheat (Triticum aestivum). PLoS One 2012; 7:e33234. [PMID: 22457747 PMCID: PMC3310869 DOI: 10.1371/journal.pone.0033234] [Citation(s) in RCA: 227] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 02/06/2012] [Indexed: 11/18/2022] Open
Abstract
The timing of flowering during the year is an important adaptive character affecting reproductive success in plants and is critical to crop yield. Flowering time has been extensively manipulated in crops such as wheat (Triticum aestivum L.) during domestication, and this enables them to grow productively in a wide range of environments. Several major genes controlling flowering time have been identified in wheat with mutant alleles having sequence changes such as insertions, deletions or point mutations. We investigated genetic variants in commercial varieties of wheat that regulate flowering by altering photoperiod response (Ppd-B1 alleles) or vernalization requirement (Vrn-A1 alleles) and for which no candidate mutation was found within the gene sequence. Genetic and genomic approaches showed that in both cases alleles conferring altered flowering time had an increased copy number of the gene and altered gene expression. Alleles with an increased copy number of Ppd-B1 confer an early flowering day neutral phenotype and have arisen independently at least twice. Plants with an increased copy number of Vrn-A1 have an increased requirement for vernalization so that longer periods of cold are required to potentiate flowering. The results suggest that copy number variation (CNV) plays a significant role in wheat adaptation.
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Affiliation(s)
- Aurora Díaz
- John Innes Centre, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - Meluleki Zikhali
- John Innes Centre, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - Adrian S. Turner
- John Innes Centre, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - Peter Isaac
- iDNA Genetics Ltd., The Norwich BioIncubator, Norwich Research Park, Norwich, United Kingdom
| | - David A. Laurie
- John Innes Centre, Norwich Research Park, Norwich, Norfolk, United Kingdom
- * E-mail:
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19
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Le Gouis J, Bordes J, Ravel C, Heumez E, Faure S, Praud S, Galic N, Remoué C, Balfourier F, Allard V, Rousset M. Genome-wide association analysis to identify chromosomal regions determining components of earliness in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:597-611. [PMID: 22065067 DOI: 10.1007/s00122-011-1732-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 10/14/2011] [Indexed: 05/18/2023]
Abstract
The modification of flowering date is considered an important way to escape the current or future climatic constraints that affect wheat crops. A better understanding of its genetic bases would enable a more efficient and rapid modification through breeding. The objective of this study was to identify chromosomal regions associated with earliness in wheat. A 227-wheat core collection chosen to be highly contrasted for earliness was characterized for heading date. Experiments were conducted in controlled conditions and in the field for 3 years to break down earliness in the component traits: photoperiod sensitivity, vernalization requirement and narrow-sense earliness. Whole-genome association mapping was carried out using 760 molecular markers and taking into account the five ancestral group structure. We identified 62 markers individually associated to earliness components corresponding to 33 chromosomal regions. In addition, we identified 15 other significant markers and seven more regions by testing marker pair interactions. Co-localizations were observed with the Ppd-1, Vrn-1 and Rht-1 candidate genes. Using an independent set of lines to validate the model built for heading date, we were able to explain 34% of the variation using the structure and the significant markers. Results were compared with already published data using bi-parental populations giving an insight into the genetic architecture of flowering time in wheat.
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Affiliation(s)
- J Le Gouis
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 234 Avenue du Brézet, 63 100, Clermont-Ferrand, France.
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20
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Borràs-Gelonch G, Rebetzke GJ, Richards RA, Romagosa I. Genetic control of duration of pre-anthesis phases in wheat (Triticum aestivum L.) and relationships to leaf appearance, tillering, and dry matter accumulation. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:69-89. [PMID: 21920907 PMCID: PMC3245455 DOI: 10.1093/jxb/err230] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The duration of pre-anthesis developmental phases is of interest in breeding for improved adaptation and yield potential in temperate cereals. Yet despite numerous studies on the genetic control of anthesis (flowering) time and floral initiation, little is known about the genetic control of other pre-anthesis phases. Furthermore, little is known about the effect that changes in the duration of pre-anthesis phases could have on traits related to leaf appearance and tillering, or dry matter accumulation before terminal spikelet initiation (TS). The genetic control of the leaf and spikelet initiation phase (LS; from sowing to TS), the stem elongation phase (SE; from TS to anthesis), and, within the latter, from TS to flag leaf appearance and from then to anthesis, was studied in two doubled-haploid, mapping bread wheat populations, Cranbrook × Halberd and CD87 × Katepwa, in two field experiments (ACT and NSW, Australia). The lengths of phases were estimated from measurements of both TS and the onset of stem elongation. Dry weight per plant before TS, rate of leaf appearance, tillering rate, maximum number of tillers and number of leaves, and dry weight per plant at TS were also estimated in the Cranbrook × Halberd population. More genomic regions were identified for the length of the different pre-anthesis phases than for total time to anthesis. Although overall genetic correlations between LS and SE were significant and positive, independent genetic variability between LS and SE, and several quantitative trait loci (QTLs) with different effects on both phases were found in the two populations. Several of these QTLs (which did not seem to coincide with reported major genes) could be of interest for breeding purposes since they were only significant for either LS or SE. There was no relationship between LS and the rate of leaf appearance. LS was strongly and positively correlated with dry weight at TS but only slightly negatively correlated with early vigour (dry weight before TS). Despite significant genetic correlations between LS and some tillering traits, shortening LS so as to lengthen SE without modifying total time to anthesis would not necessarily reduce tillering capacity, as QTLs for tillering traits did not coincide with those QTLs significant only for LS or SE. Therefore, the study of different pre-anthesis phases is relevant for a better understanding of genetic factors regulating developmental time and may offer new tools for fine-tuning it in breeding for both adaptability and yield potential.
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Affiliation(s)
- Gisela Borràs-Gelonch
- Department of Crop and Forest Sciences, University of Lleida, and Centre UdL-IRTA, Alcalde Rovira Roure, 191, 25198 Lleida, Catalonia, Spain.
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21
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Wang G, Leonard JM, Ross AS, Peterson CJ, Zemetra RS, Garland Campbell K, Riera-Lizarazu O. Identification of genetic factors controlling kernel hardness and related traits in a recombinant inbred population derived from a soft × 'extra-soft' wheat (Triticum aestivum L.) cross. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:207-21. [PMID: 21959906 DOI: 10.1007/s00122-011-1699-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Accepted: 08/29/2011] [Indexed: 05/03/2023]
Abstract
Kernel hardness or texture, used to classify wheat (Triticum aestivum L.) into soft and hard classes, is a major determinant of milling and baking quality. Wheat genotypes in the soft class that are termed 'extra-soft' (with kernel hardness in the lower end of the spectrum) have been associated with superior end-use quality. In order to better understand the relationship between kernel hardness, milling yield, and various agronomic traits, we performed quantitative trait mapping using a recombinant inbred line population derived from a cross between a common soft wheat line and a genotype classified as an 'extra-soft' line. A total of 47 significant quantitative trait loci (QTL) (LOD ≥ 3.0) were identified for nine traits with the number of QTL affecting each trait ranging from three to nine. The percentage of phenotypic variance explained by these QTL ranged from 3.7 to 50.3%. Six QTL associated with kernel hardness and break flour yield were detected on chromosomes 1BS, 4BS, 5BS, 2DS, 4DS, and 5DL. The two most important QTL were mapped onto orthologous regions on chromosomes 4DS (Xbarc1118-Rht-D1) and 4BS (Xwmc617-Rht-B1). These results indicated that the 'extra-soft' characteristic was not controlled by the Hardness (Ha) locus on chromosome 5DS. QTL for eight agronomic traits occupied two genomic regions near semi-dwarf genes Rht-D1 on chromosome 4DS and Rht-B1 on chromosome 4BS. The clustering of these QTL is either due to the pleiotropic effects of single genes or tight linkage of genes controlling these various traits.
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Affiliation(s)
- Guomei Wang
- Department of Crop and Soil Science, Oregon State University, 107 Crop Science Building, Corvallis, OR 97331-3002, USA.
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Fayt VI, Balashova IA, Sivolap YM. Mapping of QTL associated with heading time in winter wheat. CYTOL GENET+ 2011. [DOI: 10.3103/s0095452711050045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Rousset M, Bonnin I, Remoué C, Falque M, Rhoné B, Veyrieras JB, Madur D, Murigneux A, Balfourier F, Le Gouis J, Santoni S, Goldringer I. Deciphering the genetics of flowering time by an association study on candidate genes in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:907-26. [PMID: 21761163 DOI: 10.1007/s00122-011-1636-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 06/13/2011] [Indexed: 05/18/2023]
Abstract
Earliness is very important for the adaptation of wheat to environmental conditions and the achievement of high grain yield. A detailed knowledge of key genetic components of the life cycle would enable an easier control by the breeders. The objective of the study was to investigate the effect of candidate genes on flowering time. Using a collection of hexaploid wheat composed of 235 lines from diverse geographical origins, we conducted an association study for six candidate genes for flowering time and its components (vernalization sensitivity and earliness per se). The effect on the variation of earliness components of polymorphisms within the copies of each gene was tested in ANOVA models accounting for the underlying genetic structure. The collection was structured in five groups that minimized the residual covariance. Vernalization requirement and lateness tend to increase according to the mean latitude of each group. Heading date for an autumnal sowing was mainly determined by the earliness per se. Except for the Constans (CO) gene orthologous of the barley HvCO3, all gene polymorphisms had a significant impact on earliness components. The three traits used to quantify vernalization requirement were primarily associated with polymorphisms at Vrn-1 and then at Vrn-3 and Luminidependens (LD) genes. We found a good correspondence between spring/winter types and genotypes at the three homeologous copies of Vrn-1. Earliness per se was mainly explained by polymorphisms at Vrn-3 and to a lesser extent at Vrn-1, Hd-1 and Gigantea (GI) genes. Vernalization requirement and earliness as a function of geographical origin, as well as the possible role of the breeding practices in the geographical distribution of the alleles and the hypothetical adaptive value of the candidate genes, are discussed.
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Affiliation(s)
- Michel Rousset
- UMR de Génétique Végétale, INRA/CNRS/AgroParisTech/Univ. Paris XI, Ferme du Moulon, 91190 Gif sur Yvette, France.
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Alm V, Busso CS, Ergon A, Rudi H, Larsen A, Humphreys MW, Rognli OA. QTL analyses and comparative genetic mapping of frost tolerance, winter survival and drought tolerance in meadow fescue (Festuca pratensis Huds.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:369-82. [PMID: 21505831 DOI: 10.1007/s00122-011-1590-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 03/31/2011] [Indexed: 05/05/2023]
Abstract
Quantitative trait loci (QTLs) for frost and drought tolerance, and winter survival in the field, were mapped in meadow fescue (Festuca pratensis Huds.) and compared with corresponding traits in Triticeae and rice to study co-location with putatively orthologous QTLs and known abiotic stress tolerance genes. The genomes of grass species are highly macrosyntenic; however, the Festuca/Lolium and Triticeae homoeologous chromosomes 4 and 5 show major structural differences that is especially interesting in comparative genomics of frost tolerance. The locations of two frost tolerance/winter survival QTLs on Festuca chromosome 5F correspond most likely to the Fr-A1 and Fr-A2 loci on wheat homoeologous group 5A chromosomes. A QTL for long-term drought tolerance on chromosome 3F (syntenic with rice 1) support evidence from introgression of Festuca genome segments onto homoeologous Lolium chromosomes (3L) that this genome region is an excellent source of tolerance towards drought stress. The coincident location of several stress tolerance QTL in Festuca with QTL and genes in Triticeae species, notably dehydrins, CBF transcription factors and vernalisation response genes indicate the action of structural or regulatory genes conserved across evolutionarily distant species.
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Affiliation(s)
- Vibeke Alm
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
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25
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Reif JC, Maurer HP, Korzun V, Ebmeyer E, Miedaner T, Würschum T. Mapping QTLs with main and epistatic effects underlying grain yield and heading time in soft winter wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:283-292. [PMID: 21476040 DOI: 10.1007/s00122-011-1583-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 03/23/2011] [Indexed: 05/30/2023]
Abstract
There is increasing awareness that epistasis plays a role for the determination of complex traits. This study employed an association mapping approach in a large panel of 455 diverse European elite soft winter wheat lines. The genotypes were evaluated in multi-environment trials and fingerprinted with SSR markers to dissect the underlying genetic architecture of grain yield and heading time. A linear mixed model was applied to assess marker-trait associations incorporating information of covariance among relatives. Our findings indicate that main effects dominate the control of grain yield in wheat. In contrast, the genetic architecture underlying heading time is controlled by main and epistatic effects. Consequently, for heading time it is important to consider epistatic effects towards an increased selection gain in marker-assisted breeding.
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Pelgas B, Bousquet J, Meirmans PG, Ritland K, Isabel N. QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments. BMC Genomics 2011; 12:145. [PMID: 21392393 PMCID: PMC3068112 DOI: 10.1186/1471-2164-12-145] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 03/10/2011] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be validated from one experiment to another. The aim of our study was to overcome this limitation by basing QTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs across pedigrees, years, and environments. RESULTS Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500 clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtained using a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers.For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs) were observed for bud flush, 52 for bud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11, 13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealed spatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted, indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were also underlined by recent genome scans or expression profile studies.Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from 2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance could be accounted for by QTLs for bud flush or bud set, and up to 59% for height growth. CONCLUSIONS This study provides a basic understanding of the genomic architecture related to bud flush, bud set, and height growth in a conifer species, and a useful indicator to compare with Angiosperms. It will serve as a basic reference to functional and association genetic studies of adaptation and growth in Picea taxa. The putative QTNs identified will be tested for associations in natural populations, with potential applications in molecular breeding and gene conservation programs. QTLs mapping consistently across years and environments could also be the most important targets for breeding, because they represent genomic regions that may be least affected by G × E interactions.
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Affiliation(s)
- Betty Pelgas
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Québec, G1V 4C7, Canada
- Arborea and Canada Research Chair in Forest and Environmental Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec, G1V OA6, Canada
| | - Jean Bousquet
- Arborea and Canada Research Chair in Forest and Environmental Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec, G1V OA6, Canada
| | - Patrick G Meirmans
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Québec, G1V 4C7, Canada
- Current address: Institute of Biodiversity and Ecosystem Dynamics, Universiteit van Amsterdam, PO Box 94248, 1090GE Amsterdam, The Netherlands
| | - Kermit Ritland
- Department of Forest Science, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Québec, G1V 4C7, Canada
- Arborea and Canada Research Chair in Forest and Environmental Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec, G1V OA6, Canada
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Chao S, Dubcovsky J, Dvorak J, Luo MC, Baenziger SP, Matnyazov R, Clark DR, Talbert LE, Anderson JA, Dreisigacker S, Glover K, Chen J, Campbell K, Bruckner PL, Rudd JC, Haley S, Carver BF, Perry S, Sorrells ME, Akhunov ED. Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.). BMC Genomics 2010; 11:727. [PMID: 21190581 PMCID: PMC3020227 DOI: 10.1186/1471-2164-11-727] [Citation(s) in RCA: 177] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 12/29/2010] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico. RESULTS Most of the wheat oligo pool assay (OPA) SNPs that were polymorphic within the complete set of 478 cultivars were also polymorphic in all subpopulations. Higher levels of genetic differentiation were observed among wheat lines within populations than among populations. A total of nine genetically distinct clusters were identified, suggesting that some of the pre-defined populations shared significant proportion of genetic ancestry. Estimates of population structure (F(ST)) at individual loci showed a high level of heterogeneity across the genome. In addition, seven genomic regions with elevated F(ST) were detected between the spring and winter wheat populations. Some of these regions overlapped with previously mapped flowering time QTL. Across all populations, the highest extent of significant LD was observed in the wheat D-genome, followed by lower LD in the A- and B-genomes. The differences in the extent of LD among populations and genomes were mostly driven by differences in long-range LD ( > 10 cM). CONCLUSIONS Genome- and population-specific patterns of genetic differentiation and LD were discovered in the populations of wheat cultivars from different geographic regions. Our study demonstrated that the estimates of population structure between spring and winter wheat lines can identify genomic regions harboring candidate genes involved in the regulation of growth habit. Variation in LD suggests that breeding and selection had a different impact on each wheat genome both within and among populations. The higher extent of LD in the wheat D-genome versus the A- and B-genomes likely reflects the episodes of recent introgression and population bottleneck accompanying the origin of hexaploid wheat. The assessment of LD and population structure in this assembled panel of diverse lines provides critical information for the development of genetic resources for genome-wide association mapping of agronomically important traits in wheat.
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Affiliation(s)
- Shiaoman Chao
- USDA ARS Genotyping Laboratory, Biosciences Research Laboratory, Fargo, ND, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Rustam Matnyazov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
- Institute of Biochemistry and Genetics, RAS, Ufa Russia
| | | | - Luther E Talbert
- Department of Plant Sciences, Montana State University, Bozeman, MT, USA
| | - James A Anderson
- Dept. of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | | | - Karl Glover
- Plant Science Department, South Dakota State University, Brookings, SD, USA
| | - Jianli Chen
- University of Idaho Aberdeen Research & Extension Center, Aberdeen ID, USA
| | - Kim Campbell
- USDA-ARS Wheat Genetics, Quality, Physiology & Disease Research Unit, Washington State University, Pullman WA, USA
| | | | - Jackie C Rudd
- Texas AgriLife Research and Extension Center, Amarillo, TX, USA
| | - Scott Haley
- Soil and Crop Sciences Department, Colorado State University, Fort Collins, CO, USA
| | - Brett F Carver
- Oklahoma State University, Department of Plant and Soil Sciences, Stillwater, OK, USA
| | | | - Mark E Sorrells
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Eduard D Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
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Bonnin I, Rousset M, Madur D, Sourdille P, Dupuits C, Brunel D, Goldringer I. FT genome A and D polymorphisms are associated with the variation of earliness components in hexaploid wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:383-94. [PMID: 18040656 DOI: 10.1007/s00122-007-0676-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Accepted: 11/08/2007] [Indexed: 05/08/2023]
Abstract
The transition from vegetative to floral meristems in higher plants is determined by the coincidence of internal and environmental signals. Contrary to the photoperiod pathway, convergent evolution of the cold-dependent pathway has implicated different genes between dicots and monocots. Whereas no association between natural variation in vernalization requirement and Flowering time locus T (FT) gene polymorphism has been described in Arabidopsis, recent studies in Triticeae suggest implication of orthologous copies of FT in the cold response. In our study, we show that nucleotide polymorphisms on A and D copies of the wheat FT gene were associated with variations for heading date in a collection of 239 lines representing diverse geographical origins and status (landraces, old or recent cultivars). Interestingly, polymorphisms in the non-coding intronic region were strongly associated to flowering variation observed on plants grown without vernalization. But differently from VRN1, no epistatic interaction between FT homeologous copies was revealed. In agreement with the results of association study, the A and D copies of FT were mapped in regions including major QTLs for earliness traits in hexaploid wheat. This work, by identifying additional homeoalleles involved in wheat vernalization pathway, will contribute to a better understanding of the control of flowering, hence providing tools for the breeding of varieties with enhanced adaptation to changing environments.
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Affiliation(s)
- Isabelle Bonnin
- UMR de Génétique Végétale, INRA/CNRS/UPS/INA-PG, Ferme du Moulon, 91190, Gif/Yvette, France.
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29
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Lewis S, Faricelli ME, Appendino ML, Valárik M, Dubcovsky J. The chromosome region including the earliness per se locus Eps-Am1 affects the duration of early developmental phases and spikelet number in diploid wheat. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:3595-607. [PMID: 18836186 PMCID: PMC2561150 DOI: 10.1093/jxb/ern209] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Revised: 07/10/2008] [Accepted: 07/21/2008] [Indexed: 05/20/2023]
Abstract
Earliness per se genes are those that regulate flowering time independently of vernalization and photoperiod, and are important for the fine tuning of flowering time and for the wide adaptation of wheat to different environments. The earliness per se locus Eps-A(m)1 was recently mapped within a 0.8 cM interval on chromosome 1A(m)L of diploid wheat Triticum monococcum L., and it was shown that its effect was modulated by temperature. In this study, this precise mapping information was used to characterize the effect of the Eps-A(m)1 region on both duration of different developmental phases and spikelet number. Near isogenic lines (NILs) carrying the Eps-A(m)1-l allele from the cultivated accession DV92 had significantly longer vegetative and spike development phases (P<0.0001) than NILs carrying the Eps-A(m)1-e allele from the wild accession G3116. These differences were paralleled by a significant increase in the number of spikelets per spike, in both greenhouse and field experiments (P<0.0001). Significant interactions between temperature and Eps-A(m)1 alleles were detected for heading time (P<0.0001) but not for spikelet number (P=0.67). Experiments using NILs homozygous for chromosomes with recombination events within the 0.8 cM Eps-A(m)1 region showed that the differences in number of spikelets per spike were linked to the differences in heading time controlled by the Eps-A(m)1 locus. These results indicate that the differences in these two traits are either pleiotropic effects of a single gene or the effect of closely linked genes. A similar effect on spikelet number was detected in the distal region of chromosome 1AL in common wheat (T. aestivum L.).
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Affiliation(s)
- S. Lewis
- Instituto de Recursos Biológicos, INTA, Villa Udaondo, (1686) Hurlingham, Buenos Aires, Argentina
| | - M. E. Faricelli
- Department of Plant Sciences, University of California, Davis, CA 95616-8515, USA
| | - M. L. Appendino
- Cátedra de Genética, Facultad de Agronomía, Universidad de Buenos Aires, (1417) Buenos Aires, Argentina
| | - M. Valárik
- Department of Plant Sciences, University of California, Davis, CA 95616-8515, USA
- Laboratory of Molecular Cytogenetics and Ctyometry, Institute of Experimental Botany, Olomouc, Czech Republic
| | - J. Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA 95616-8515, USA
- To whom correspondence should be addressed: E-mail:
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30
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Hanocq E, Laperche A, Jaminon O, Lainé AL, Le Gouis J. Most significant genome regions involved in the control of earliness traits in bread wheat, as revealed by QTL meta-analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:569-84. [PMID: 17171391 DOI: 10.1007/s00122-006-0459-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 11/06/2006] [Indexed: 05/13/2023]
Abstract
Earliness is one of the most important adaptation traits in plant breeding. Our purpose was to identify the genome regions of bread wheat involved in the control of earliness and its three components: photoperiod sensitivity (PS), vernalization requirement (VR) and intrinsic earliness (IE). A QTL meta-analysis was carried out to examine the replicability of QTL across 13 independent studies and to propose meta-QTL (MQTL). Initial QTL were projected on a recent consensus map (2004). Quality criteria were proposed to assess the reliability of this projection. These criteria were based on the distances between markers in the QTL regions. Chromosomes of groups 2 and 5 had a greater incidence on earliness control as they carry the known, major genes Ppd and Vrn. Other chromosome regions played an intermediate role in earliness control: 4A [heading date (HD) Meta-QTL], 4B (HD MQTL), 2B (VR MQTL) and 5B (IE MQTL). Markers at this four MQTL should prove helpful in marker-assisted selection, to better control earliness.
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Affiliation(s)
- E Hanocq
- Unité Mixte de Recherche INRA/USTL 1281, Stress abiotiques et différenciation des végétaux cultivés, Estrées-Mons, Institut National de la Recherche Agronomique (INRA), BP 50136, 80203, Péronne Cedex, France.
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Kuchel H, Hollamby G, Langridge P, Williams K, Jefferies SP. Identification of genetic loci associated with ear-emergence in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:1103-12. [PMID: 16896709 DOI: 10.1007/s00122-006-0370-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Accepted: 07/06/2006] [Indexed: 05/11/2023]
Abstract
A doubled haploid population constructed from a cross between the South Australian wheat cultivars 'Trident' and 'Molineux' was grown under winter field conditions, under field conditions over summer and under artificial light both with and without vernalisation. The duration from planting to ear-emergence was recorded and QTL associated with heading date were detected using a previously constructed genetic linkage map. Associations were shown with chromosomal regions syntenous to previously identified photoperiod (Ppd-B1) and vernalisation (Vrn-A1) sensitive loci. Additional QTL associated with time to heading were also identified on chromosomes 1A, 2A, 2B, 6D, 7A and 7B. Comparisons between the genetic associations observed under the different growing conditions allowed the majority of these loci to be classified as having either photoperiod-sensitive, vernalisation-sensitive or earliness per se actions. The identification of a photoperiod-sensitive QTL on chromosome 1A provides evidence for a wheat gene possibly homoeologous to Ppd-H2 previously identified on chromosome 1H of barley. The occurrence of a putative major gene for photoperiod sensitivity observed on chromosome 7A is presented. The combined additive effects at these loci accounted for more than half the phenotypic variance in the duration from planting to ear-emergence in this population. The possible role of these loci on the adaptation of wheat in Australia is discussed.
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Affiliation(s)
- H Kuchel
- Australian Grain Technologies Pty Ltd, University of Adelaide, Roseworthy Campus, Roseworthy, SA 5371, Australia.
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32
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Kosmala A, Zwierzykowski Z, Gasior D, Rapacz M, Zwierzykowska E, Humphreys MW. GISH/FISH mapping of genes for freezing tolerance transferred from Festuca pratensis to Lolium multiflorum. Heredity (Edinb) 2006; 96:243-51. [PMID: 16449983 DOI: 10.1038/sj.hdy.6800787] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The first backcross breeding programme for the transfer of freezing-tolerance genes from winter hardy Festuca pratensis to winter-sensitive Lolium multiflorum is described. A partly fertile, triploid F(1) hybrid F. pratensis (2n=2x=14) x L. multiflorum (2n=4x=28) was employed initially, and after two backcrosses to L. multiflorum (2x) a total of 242 backcross two (BC(2)) plants were generated. Genomic in situ hybridisation (GISH) was performed on 61 BC(2) plants selected for their good growth and winter survival characters in the spring following one Polish winter (2000-2001). Among the winter survivors, diploid chromosome numbers were present in 80% of plants. An appropriate single Festuca introgression in an otherwise undisturbed Lolium genome could provide increased freezing tolerance without compromise to the good growth and plant vigour found in Lolium. Among all the diploids, a total of 20 individuals were identified, each with a single F. pratensis chromosome segment. Another diploid plant contained 13 Lolium chromosomes and a large metacentric F. pratensis chromosome, identified as chromosome 4, with two large distal Lolium introgressions on each chromosome arm. Three of the diploid BC(2), including the genotype with Festuca chromosome 4 DNA sequences, were found to have freezing tolerance in excess of that of L. multiflorum, and in one case in excess of the F. pratensis used as control. A detailed cytological analysis combining GISH and fluorescence in situ hybridisation analyses with rDNA probes revealed that the other two freezing-tolerant genotypes carried a Festuca chromosome segment at the same terminal location on the non-satellite arm of Lolium chromosome 2.
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Affiliation(s)
- A Kosmala
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland.
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33
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Ergon A, Fang C, Jørgensen Ø, Aamlid TS, Rognli OA. Quantitative trait loci controlling vernalisation requirement, heading time and number of panicles in meadow fescue (Festuca pratensis Huds.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:232-42. [PMID: 16235049 DOI: 10.1007/s00122-005-0115-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Accepted: 09/14/2005] [Indexed: 05/04/2023]
Abstract
The "BF14/16xHF2/7" mapping population of meadow fescue (Festuca pratensis Huds.) was characterised for number of panicles produced by non-vernalised plants in the field, vernalisation requirement (number of weeks at 6 degrees C and 8 h photoperiod), as well as days to heading, number of panicles and proportion of shoots heading after a 12 weeks vernalisation treatment. Quantitative trait loci (QTLs) were identified and compared to QTLs and genes related to the induction of flowering in cereals and grasses. A region on chromosome 1F affected days to heading and the proportion of shoots heading. Chromosome 4F appeared to have several genes with a strong effect on vernalisation requirement. The strongest effects were located in the proximal end of 4F and may correspond to the earliness per se (eps) QTL eps6L.2 in barley and a heading time QTL in perennial ryegrass. A part of the meadow fescue orthologue of VRN1 was sequenced and mapped to another region of 4F that also had a strong effect on vernalisation requirement. The proximal end of chromosome 5F had QTLs for days to heading and proportion of heading shoots. Syntenic regions in wheat and barley contain eps-loci. A QTL for number of panicles in the field and a QTL for proportion of heading shoots were present on chromosome 6. A region on 7F affected the variation in number of panicles among plants without a vernalisation requirement, and is syntenic to regions in perennial ryegrass, barley and rice containing orthologues of Arabidopsis thaliana CO.
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Affiliation(s)
- A Ergon
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 As, Norway
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Kane NA, Danyluk J, Tardif G, Ouellet F, Laliberté JF, Limin AE, Fowler DB, Sarhan F. TaVRT-2, a member of the StMADS-11 clade of flowering repressors, is regulated by vernalization and photoperiod in wheat. PLANT PHYSIOLOGY 2005; 138:2354-63. [PMID: 16024692 PMCID: PMC1183421 DOI: 10.1104/pp.105.061762] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The initiation of the reproductive phase in winter cereals is delayed during winter until favorable growth conditions resume in the spring. This delay is modulated by low temperature through the process of vernalization. The molecular and genetic bases of the interaction between environmental factors and the floral transition in these species are still unknown. However, the recent identification of the wheat (Triticum aestivum L.) TaVRT-1 gene provides an opportunity to decipher the molecular basis of the flowering-time regulation in cereals. Here, we describe the characterization of another gene, named TaVRT-2, possibly involved in the flowering pathway in wheat. Molecular and phylogenetic analyses indicate that the gene encodes a member of the MADS-box transcription factor family that belongs to a clade responsible for flowering repression in several species. Expression profiling of TaVRT-2 in near-isogenic lines and different genotypes with natural variation in their response to vernalization and photoperiod showed a strong relationship with floral transition. Its expression is up-regulated in the winter genotypes during the vegetative phase and in photoperiod-sensitive genotypes during short days, and is repressed by vernalization to a level that allows the transition to the reproductive phase. Protein-protein interaction studies revealed that TaVRT-2 interacts with proteins encoded by two important vernalization genes (TaVRT-1/VRN-1 and VRN-2) in wheat. These results support the hypothesis that TaVRT-2 is a putative repressor of the floral transition in wheat.
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Affiliation(s)
- Ndjido A Kane
- Département des Sciences Biologiques, Université du Québec à Montréal, Montreal, Quebec, Canada H3C 3P8
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Suenaga K, Khairallah M, William HM, Hoisington DA. A new intervarietal linkage map and its application for quantitative trait locus analysis of "gigas" features in bread wheat. Genome 2005; 48:65-75. [PMID: 15729398 DOI: 10.1139/g04-092] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A doubled-haploid (DH) population from an intervarietal cross between the Japanese cultivar 'Fukuho-komugi' and the Israeli wheat line 'Oligoculm' was produced by means of wheat × maize crosses. One hundred seven DH lines were genotyped to construct a simple sequence repeat (SSR) based linkage map with RFLP, RAPD, and inter-simple sequence repeat markers. Out of 570 loci genotyped, 330 were chosen based on their positions on the linkage map to create a "framework" map for quantitative trait locus (QTL) analysis. Among the 28 linkage groups identified, 25 were assigned to the 21 chromosomes of wheat. The total map length was 3948 cM, including the three unassigned linkage groups (88 cM), and the mean interval between loci was 12.0 cM. Loci with segregation distortion were clustered on chromosomes 1A, 4B, 4D, 5A, 6A, 6B, and 6D. After vernalization, the DH lines were evaluated for spike number per plant (SN) and spike length (SL) in a greenhouse under 24-h daylength to assess the "gigas" features (extremely large spikes and leaves) of 'Oligoculm'. The DH lines were also autumn-sown in the field in two seasons (1990–1991 and 1997–1998) for SN and SL evaluation. QTL analysis was performed by composite interval mapping (CIM) with the framework map to detect QTLs for SN and SL. A major QTL on 1AS, which was stable in both greenhouse and field conditions, was found to control SN. This QTL was close to the glume pubescence locus (Hg) and explained up to 62.9% of the total phenotypic variation. The 'Oligoculm' allele restricted spike number. The SSR locus Xpsp2999 was the closest locus to this QTL and is considered to be a possible marker for restricted tillering derived from 'Oligoculm'. Eight QTLs were detected for SL. The largest QTL detected on 2DS was common to the greenhouse and field environments. It explained up to 33.3% of the total phenotypic variation. The second largest QTL on 1AS was common to the greenhouse and the 1997–1998 season. The position of this QTL was close to that for the SN detected on 1AS. The association between SN and SL is discussed.Key words: linkage map, microsatellite, QTL, spike length, spike number.
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Affiliation(s)
- Kazuhiro Suenaga
- International Maize and Wheat Improvement Center, Mexico, D.F., Mexico.
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Hanocq E, Niarquin M, Heumez E, Rousset M, Le Gouis J. Detection and mapping of QTL for earliness components in a bread wheat recombinant inbred lines population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 110:106-15. [PMID: 15551039 DOI: 10.1007/s00122-004-1799-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Accepted: 08/12/2004] [Indexed: 05/02/2023]
Abstract
Earliness, an adaptative trait and factor of variation for agronomic characters, is a major trait in plant breeding. Its constituent traits, photoperiod sensitivity (PS), vernalization requirement (VR) and intrinsic earliness (IE), are largely under independent genetic controls. Mapping of major genes and quantitative trait loci (QTL) controlling these components is in progress. Most of the studies focusing on earliness considered it as a whole or through one (or two) of its components. The purpose of this study was to detect and map QTL for the three traits together through an experimental design combining field trials and controlled growth conditions. QTL were mapped in a population of F(7) recombinant inbred lines derived by single-seed descent from a cross between two French varieties, 'Renan' and 'Recital'. A map was previously constructed, based on 194 lines and 254 markers, covering about 77% of the genome. Globally, 13 QTL with a LOD>2.5 were detected, of which four control PS, five control VR and four control IE. Two major photoperiod sensitive QTL, together explaining more than 31% of the phenotypic variation, were mapped on chromosomes 2B and 2D, at the same position as the two major genes Ppd-B1 and Ppd-D1. One major VR QTL explaining (depending on the year) 21.8-39.6% of the phenotypic variation was mapped on 5A. Among the other QTL, two QTL of PS and VR not referenced so far were detected on 5A and 6D, respectively. A VR QTL already detected on 2B in a connected population was confirmed.
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Affiliation(s)
- E Hanocq
- Institut National de la Recherche Agronomique (INRA), Unité de Génétique et Amélioration des Plantes, B.P. 50136, 80203 Péronne Cedex, France.
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Jermstad KD, Bassoni DL, Jech KS, Ritchie GA, Wheeler NC, Neale DB. Mapping of Quantitative Trait Loci Controlling Adaptive Traits in Coastal Douglas Fir. III. Quantitative Trait Loci-by-Environment Interactions. Genetics 2003; 165:1489-506. [PMID: 14668397 PMCID: PMC1462859 DOI: 10.1093/genetics/165.3.1489] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Quantitative trait loci (QTL) were mapped in the woody perennial Douglas fir (Pseudotsuga menziesii var. menziesii [Mirb.] Franco) for complex traits controlling the timing of growth initiation and growth cessation. QTL were estimated under controlled environmental conditions to identify QTL interactions with photoperiod, moisture stress, winter chilling, and spring temperatures. A three-generation mapping population of 460 cloned progeny was used for genetic mapping and phenotypic evaluations. An all-marker interval mapping method was used for scanning the genome for the presence of QTL and single-factor ANOVA was used for estimating QTL-by-environment interactions. A modest number of QTL were detected per trait, with individual QTL explaining up to 9.5% of the phenotypic variation. Two QTL-by-treatment interactions were found for growth initiation, whereas several QTL-by-treatment interactions were detected among growth cessation traits. This is the first report of QTL interactions with specific environmental signals in forest trees and will assist in the identification of candidate genes controlling these important adaptive traits in perennial plants.
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Affiliation(s)
- Kathleen D Jermstad
- Institute of Forest Genetics, Pacific Southwest Research Station, U.S. Department of Agriculture Forest Service, Placerville, California 95667, USA
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Griffiths S, Dunford RP, Coupland G, Laurie DA. The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis. PLANT PHYSIOLOGY 2003; 131:1855-67. [PMID: 12692345 PMCID: PMC166942 DOI: 10.1104/pp.102.016188] [Citation(s) in RCA: 318] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2002] [Revised: 12/03/2002] [Accepted: 12/12/2002] [Indexed: 05/18/2023]
Abstract
The CO (CONSTANS) gene of Arabidopsis has an important role in the regulation of flowering by photoperiod. CO is part of a gene family with 17 members that are subdivided into three classes, termed Group I to III here. All members of the family have a CCT (CO, CO-like, TOC1) domain near the carboxy terminus. Group I genes, which include CO, have two zinc finger B-boxes near the amino terminus. Group II genes have one B-box, and Group III genes have one B-box and a second diverged zinc finger. Analysis of rice (Oryza sativa) genomic sequence identified 16 genes (OsA-OsP) that were also divided into these three groups, showing that their evolution predates monocot/dicot divergence. Eight Group I genes (HvCO1-HvCO8) were isolated from barley (Hordeum vulgare), of which two (HvCO1 and HvCO2) were highly CO like. HvCO3 and its rice counterpart (OsB) had one B-box that was distantly related to Group II genes and was probably derived by internal deletion of a two B-box Group I gene. Sequence homology and comparative mapping showed that HvCO1 was the counterpart of OsA (Hd1), a major determinant of photoperiod sensitivity in rice. Major genes determining photoperiod response have been mapped in barley and wheat (Triticum aestivum), but none corresponded to CO-like genes. Thus, selection for variation in photoperiod response has affected different genes in rice and temperate cereals. The peptides of HvCO1, HvCO2 (barley), and Hd1 (rice) show significant structural differences from CO, particularly amino acid changes that are predicted to abolish B-box2 function, suggesting an evolutionary trend toward a one-B-box structure in the most CO-like cereal genes.
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Affiliation(s)
- Simon Griffiths
- John Innes Centre, Norwich Research Park, Colney, United Kingdom
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Gervais L, Dedryver F, Morlais JY, Bodusseau V, Negre S, Bilous M, Groos C, Trottet M. Mapping of quantitative trait loci for field resistance to Fusarium head blight in an European winter wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 106:961-70. [PMID: 12671743 DOI: 10.1007/s00122-002-1160-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2002] [Accepted: 08/20/2002] [Indexed: 05/20/2023]
Abstract
Fusarium head blight (FHB) caused by Fusarium culmorum is an economically important disease of wheat that may cause serious yield and quality losses under favorable climate conditions. The development of disease-resistant cultivars is the most effective control strategy. Worldwide, there is heavy reliance on the resistance pool originating from Asian wheats, but excellent field resistance has also been observed among European winter wheats. The objective of this study was to map and characterize quantitative traits loci (QTL) of resistance to FHB among European winter wheats. A population of 194 recombinant inbred lines (RILs) was genotyped from a cross between two winter wheats Renan (resistant)/Récital (susceptible) with microsatellites, AFLP and RFLP markers. RILs were assessed under field conditions For 3 years in one location. Nine QTLs were detected, and together they explained 30-45% of the variance, depending on the year. Three of the QTLs were stable over the 3 years. One stable QTL, QFhs.inra.2b, was mapped to chromosome 2B and two QTLs QFhs.inra.5a2 and QFhs.inra5a3, to chromosome 5A; each of these QTLs explained 6.9-18.6% of the variance. Other QTLs were identified on chromosome 2A, 3A, 3B, 5D, and 6D, but these had a smaller effect on FHB resistance. One of the two QTLs on chromosome 5A was linked to gene B1 controlling the presence of awns. Overlapping QTLs for FHB resistance were those for plant height or/and flowering time. Our results confirm that wheat chromosomes 2A, 3A, 3B, and 5A carry FHB resistance genes, and new resistance factors were identified on chromosome arms 2BS and 5AL. Markers flanking these QTLs should be useful tools for combining the resistance to FHB of Asian and European wheats to increase the resistance level of cultivars.
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Affiliation(s)
- L Gervais
- Institut National de la Recherche Agronomique (INRA), UMR INRA ENSAR d'Amélioration des Plantes et Biotechnologies Végétales, Domaine de la Motte 35327, 35653 Le Rheu Cedex, France.
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