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Neupane B, Bisek B, Marais F. A diallel study to detect genetic background variation for FHB resistance in winter wheat. Sci Rep 2024; 14:4614. [PMID: 38409167 PMCID: PMC10897133 DOI: 10.1038/s41598-024-53710-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 02/04/2024] [Indexed: 02/28/2024] Open
Abstract
Breeding for resistance to Fusarium head blight (FHB) relies strongly on a limited number of larger-effect resistance QTL that have been mapped and associated with nearby markers. Smaller-effect (background) resistance QTL may also contribute moderate levels of resistance yet are mostly poorly characterized. Overall resistance of a genotype is determined by the combined action of both types of resistance QTL. This study aimed to identify well-adapted, advanced hard red winter (HRW) wheat breeding lines with useful background resistance QTL. A diallel trial consisting of 11 parents and 55 non-reciprocal F1 hybrids was tested for Type II FHB resistance in a replicated greenhouse experiment. Significant differences were detected among entries for disease severity (DS), general combining ability (GCA) and specific combining ability (SCA) with four parents being identified as the best general combiners with lowest DS. The ratio of GCA:SCA effects suggested that additive QTL effects were of primary importance. Overall, resistance QTL showed incomplete dominance, an excess of dominant alleles, and a greater contribution of positive effect genes. F2 of the six best F1 hybrids with the lowest DS were compared in a second greenhouse FHB trial to select possible transgressive segregates for continued evaluation and line development.
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Affiliation(s)
- Bipin Neupane
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA.
| | - Bradley Bisek
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Francois Marais
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
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Esposito S, Vitale P, Taranto F, Saia S, Pecorella I, D'Agostino N, Rodriguez M, Natoli V, De Vita P. Simultaneous improvement of grain yield and grain protein concentration in durum wheat by using association tests and weighted GBLUP. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:242. [PMID: 37947927 DOI: 10.1007/s00122-023-04487-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
KEY MESSAGE Simultaneous improvement for GY and GPC by using GWAS and GBLUP suggested a significant application in durum wheat breeding. Despite the importance of grain protein concentration (GPC) in determining wheat quality, its negative correlation with grain yield (GY) is still one of the major challenges for breeders. Here, a durum wheat panel of 200 genotypes was evaluated for GY, GPC, and their derived indices (GPD and GYD), under eight different agronomic conditions. The plant material was genotyped with the Illumina 25 k iSelect array, and a genome-wide association study was performed. Two statistical models revealed dozens of marker-trait associations (MTAs), each explaining up to 30%. phenotypic variance. Two markers on chromosomes 2A and 6B were consistently identified by both models and were found to be significantly associated with GY and GPC. MTAs identified for phenological traits co-mapped to well-known genes (i.e., Ppd-1, Vrn-1). The significance values (p-values) that measure the strength of the association of each single nucleotide polymorphism marker with the target traits were used to perform genomic prediction by using a weighted genomic best linear unbiased prediction model. The trained models were ultimately used to predict the agronomic performances of an independent durum wheat panel, confirming the utility of genomic prediction, although environmental conditions and genetic backgrounds may still be a challenge to overcome. The results generated through our study confirmed the utility of GPD and GYD to mitigate the inverse GY and GPC relationship in wheat, provided novel markers for marker-assisted selection and opened new ways to develop cultivars through genomic prediction approaches.
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Affiliation(s)
- Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, SS 673 Meters 25200, 71122, Foggia, Italy
| | - Paolo Vitale
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, SS 673 Meters 25200, 71122, Foggia, Italy
- Department of Agriculture, Food, Natural Science, Engineering, University of Foggia, Via Napoli 25, 71122, Foggia, Italy
| | - Francesca Taranto
- Institute of Biosciences and Bioresources (CNR-IBBR), Via Amendola 165/A, 70126, Bari, Italy
| | - Sergio Saia
- Department of Veterinary Sciences, University of Pisa, 56129, Pisa, Italy
| | - Ivano Pecorella
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, SS 673 Meters 25200, 71122, Foggia, Italy
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Monica Rodriguez
- Department of Agriculture, University of Sassari, Viale Italia, 39, 07100, Sassari, Italy
| | - Vincenzo Natoli
- Genetic Services SRL, Contrada Catenaccio, snc, 71026, Deliceto, FG, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, SS 673 Meters 25200, 71122, Foggia, Italy.
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Taranto F, Esposito S, De Vita P. Genomics for Yield and Yield Components in Durum Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:2571. [PMID: 37447132 DOI: 10.3390/plants12132571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
In recent years, many efforts have been conducted to dissect the genetic basis of yield and yield components in durum wheat thanks to linkage mapping and genome-wide association studies. In this review, starting from the analysis of the genetic bases that regulate the expression of yield for developing new durum wheat varieties, we have highlighted how, currently, the reductionist approach, i.e., dissecting the yield into its individual components, does not seem capable of ensuring significant yield increases due to diminishing resources, land loss, and ongoing climate change. However, despite the identification of genes and/or chromosomal regions, controlling the grain yield in durum wheat is still a challenge, mainly due to the polyploidy level of this species. In the review, we underline that the next-generation sequencing (NGS) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms, as well as genome editing technology, will revolutionize plant breeding by providing a great opportunity to capture genetic variation that can be used in breeding programs. To date, genomic selection provides a valuable tool for modeling optimal allelic combinations across the whole genome that maximize the phenotypic potential of an individual under a given environment.
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Affiliation(s)
- Francesca Taranto
- Institute of Biosciences and Bioresources (CNR-IBBR), 70126 Bari, Italy
| | - Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, 71122 Foggia, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, 71122 Foggia, Italy
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Jiang C, Xu Z, Fan X, Zhou Q, Ji G, Chen L, Yu Q, Liao S, Zhao Y, Feng B, Wang T. Identification and validation of quantitative trait loci for fertile spikelet number per spike and grain number per fertile spikelet in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:69. [PMID: 36952062 DOI: 10.1007/s00122-023-04297-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/26/2022] [Indexed: 06/18/2023]
Abstract
A major and stable QTL for fertile spikelet number per spike and grain number per fertile spikelet identified in a 4.96-Mb interval on chromosome 2A was validated in different genetic backgrounds. Fertile spikelet number per spike (FSN) and grain number per fertile spikelet (GNFS) contribute greatly to wheat yield improvement. To detect quantitative trait loci (QTL) associated with FSN and GNFS, we used a recombinant inbred line population crossed by Zhongkemai 13F10 and Chuanmai 42 in eight environments. Two Genomic regions associated with FSN were detected on chromosomes 2A and 6A using bulked segregant exome sequencing analysis. After the genetic linkage maps were constructed, four QTL QFsn.cib-2A, QFsn.cib-6A, QGnfs.cib-2A and QGnfs.cib-6A were identified in three or more environments. Among them, two major QTL QFsn.cib-2A (LOD = 4.67-9.34, PVE = 6.66-13.05%) and QGnfs.cib-2A (LOD = 5.27-11.68, PVE = 7.95-16.71%) were detected in seven and six environments, respectively. They were co-located in the same region, namely QFsn/Gnfs.cib-2A. The developed linked Kompetitive Allele Specific PCR (KASP) markers further validated this QTL in a different genetic background. QFsn/Gnfs.cib-2A showed pleiotropic effects on grain number per spike (GNS) and spike compactness (SC), and had no effect on grain weight. Since QFsn/Gnfs.cib-2A might be a new locus, it and the developed KASP markers can be used in wheat breeding. According to haplotype analysis, QFsn/Gnfs.cib-2A was identified as a target of artificial selection during wheat improvement. Based on haplotype analysis, sequence differences, spatiotemporal expression patterns, and gene annotation, the potential candidate genes for QFsn/Gnfs.cib-2A were predicted. These results provide valuable information for fine mapping and cloning gene(s) underlying QFsn/Gnfs.cib-2A.
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Affiliation(s)
- Cheng Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- College of Life Sciences, Sichuan University, Chengdu, 610064, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Guangsi Ji
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liangen Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qin Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun Zhao
- College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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Ma F, Xu Y, Wang R, Tong Y, Zhang A, Liu D, An D. Identification of major QTLs for yield-related traits with improved genetic map in wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1138696. [PMID: 37008504 PMCID: PMC10063875 DOI: 10.3389/fpls.2023.1138696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Identification of stable major quantitative trait loci (QTLs) for yield-related traits is important for yield potential improvement in wheat breeding. METHODS In the present study, we genotyped a recombinant inbred line (RIL) population using the Wheat 660K SNP array and constructed a high-density genetic map. The genetic map showed high collinearity with the wheat genome assembly. Fourteen yield-related traits were evaluated in six environments for QTL analysis. RESULTS AND DISCUSSION A total of 12 environmentally stable QTLs were identified in at least three environments, explaining up to 34.7% of the phenotypic variation. Of these, QTkw-1B.2 for thousand kernel weight (TKW), QPh-2D.1 (QSl-2D.2/QScn-2D.1) for plant height (PH), spike length (SL) and spikelet compactness (SCN), QPh-4B.1 for PH, and QTss-7A.3 for total spikelet number per spike (TSS) were detected in at least five environments. A set of Kompetitive Allele Specific PCR (KASP) markers were converted based on the above QTLs and used to genotype a diversity panel comprising of 190 wheat accessions across four growing seasons. QPh-2D.1 (QSl-2D.2/QScn-2D.1), QPh-4B.1 and QTss-7A.3 were successfully validated. Compared with previous studies, QTkw-1B.2 and QPh-4B.1 should be novel QTLs. These results provided a solid foundation for further positional cloning and marker-assisted selection of the targeted QTLs in wheat breeding programs.
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Affiliation(s)
- Feifei Ma
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Yunfeng Xu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Ruifang Wang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Aimin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Dongcheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Diaoguo An
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
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Ma C, Liu L, Liu T, Jia Y, Jiang Q, Bai H, Ma S, Li S, Wang Z. QTL Mapping for Important Agronomic Traits Using a Wheat55K SNP Array-Based Genetic Map in Tetraploid Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:847. [PMID: 36840195 PMCID: PMC9964379 DOI: 10.3390/plants12040847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Wheat yield is highly correlated with plant height, heading date, spike characteristics, and kernel traits. In this study, we used the wheat55K single nucleotide polymorphism array to genotype a recombinant inbred line population of 165 lines constructed by crossing two tetraploid wheat materials, Icaro and Y4. A genetic linkage map with a total length of 6244.51 cM was constructed, covering 14 chromosomes of tetraploid wheat. QTLs for 12 important agronomic traits, including plant height (PH), heading date (HD), awn color (AC), spike-branching (SB), and related traits of spike and kernel, were mapped in multiple environments, while combined QTL-by-environment interactions and epistatic effects were analyzed for each trait. A total of 52 major or stable QTLs were identified, among which may be some novel loci controlling PH, SB, and kernel length-width ratio (LWR), etc., with LOD values ranging from 2.51 to 54.49, thereby explaining 2.40-66.27% of the phenotypic variation. Based on the 'China Spring' and durum wheat reference genome annotations, candidate genes were predicted for four stable QTLs, QPH.nwafu-2B.2 (165.67-166.99 cM), QAC.nwafu-3A.1 (419.89-420.52 cM), QAC.nwafu-4A.1 (424.31-447.4 cM), and QLWR.nwafu-7A.1 (166.66-175.46 cM). Thirty-one QTL clusters and 44 segregation distortion regions were also detected, and 38 and 18 major or stable QTLs were included in these clusters and segregation distortion regions, respectively. These results provide QTLs with breeding application potential in tetraploid wheat that broadens the genetic basis of important agronomic traits such as PH, HD, AC, SB, etc., and benefits wheat breeding.
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Affiliation(s)
- Chao Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Le Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Tianxiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Yatao Jia
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Qinqin Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Haibo Bai
- Agricultural Bio-Technology Research Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan 750002, China
| | - Sishuang Ma
- Agricultural Bio-Technology Research Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan 750002, China
| | - Shuhua Li
- Agricultural Bio-Technology Research Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan 750002, China
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
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Diversity matters in wheat mixtures: A genomic survey of the impact of genetic diversity on the performance of 12 way durum wheat mixtures grown in two contrasted and controlled environments. PLoS One 2022; 17:e0276223. [PMID: 36490260 PMCID: PMC9733896 DOI: 10.1371/journal.pone.0276223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 10/04/2022] [Indexed: 12/13/2022] Open
Abstract
In ecology, an increase in genetic diversity within a community in natural ecosystems increases its productivity, while in evolutionary biology, kinship selection predicts that relatedness on social traits improves fitness. Varietal mixtures, where different genotypes are grown together, show contrasting results, especially for grain yield where both positive and negative effects of mixtures have been reported. To understand the effect of diversity on field performance, we grew 96 independent mixtures each composed with 12 durum wheat (Triticum turgidum ssp. durum Thell.) inbred lines, under two contrasting environmental conditions for water availability. Using dense genotyping, we imputed allelic frequencies and a genetic diversity index on more than 96000 loci for each mixture. We then analyzed the effect of genetic diversity on agronomic performance using a genome-wide approach. We explored the stress gradient hypothesis, which proposes that the greater the unfavourable conditions, the more beneficial the effect of diversity on mixture performance. We found that diversity on average had a negative effect on yield and its components while it was beneficial on grain weight. There was little support for the stress gradient theory. We discuss how to use genomic data to improve the assembly of varietal mixtures.
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Peters Haugrud AR, Zhang Q, Green AJ, Xu SS, Faris JD. Identification of stable QTL controlling multiple yield components in a durum × cultivated emmer wheat population under field and greenhouse conditions. G3 (BETHESDA, MD.) 2022; 13:6762085. [PMID: 36250796 PMCID: PMC9911061 DOI: 10.1093/g3journal/jkac281] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/27/2022] [Indexed: 11/09/2022]
Abstract
Crop yield gains are needed to keep pace with a growing global population and decreasing resources to produce food. Cultivated emmer wheat is a progenitor of durum wheat and a useful source of genetic variation for trait improvement in durum. Here, we evaluated a recombinant inbred line population derived from a cross between the North Dakota durum wheat variety Divide and the cultivated emmer wheat accession PI 272527 consisting of 219 lines. The population was evaluated in 3 field environments and 2 greenhouse experiments to identify quantitative trait locus associated with 11 yield-related traits that were expressed in a consistent manner over multiple environments. We identified 27 quantitative trait locus expressed in at least 2 field environments, 17 of which were also expressed under greenhouse conditions. Seven quantitative trait locus regions on chromosomes 1B, 2A, 2B, 3A, 3B, 6A, and 7B had pleiotropic effects on multiple yield-related traits. The previously cloned genes Q and FT-B1, which are known to be associated with development and morphology, were found to consistently be associated with multiple traits across environments. PI 272527 contributed beneficial alleles for quantitative trait locus associated with multiple traits, especially for seed morphology quantitative trait locus on chromosomes 1B, 2B, and 6A. Three recombinant inbred lines with increased grain size and weight compared to Divide were identified and demonstrated the potential for improvement of durum wheat through deployment of beneficial alleles from the cultivated emmer parent. The findings from this study provide knowledge regarding stable and robust quantitative trait locus that breeders can use for improving yield in durum wheat.
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Affiliation(s)
| | - Qijun Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Andrew J Green
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Steven S Xu
- USDA-ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Justin D Faris
- Corresponding author: Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND 58102, USA.
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Pleiotropic Effect of the compactum Gene and Its Combined Effects with Other Loci for Spike and Grain-Related Traits in Wheat. PLANTS 2022; 11:plants11141837. [PMID: 35890471 PMCID: PMC9316965 DOI: 10.3390/plants11141837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/30/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
Club wheat (Triticum aestivum ssp. compactum) with a distinctly compact spike morphology was conditioned by the dominant compactum (C) locus on chromosome 2D and resulted in a redistribution of spike yield components. The disclosure of the genetic basis of club wheat was a prerequisite for the development of widely adapted, agronomically competitive club wheat cultivars. In this study, we used a recombinant inbred line population derived from a cross between club wheat Hiller and modern cultivar Yangmai 158 to construct a genetic linkage map and identify quantitative trait loci associated with 15 morphological traits. The club allele acted in a semi-dominant manner and the C gene was mapped to 370.12–406.29 Mb physical region on the long arm of 2D. Apart from compact spikes, C exhibited a pleiotropic effect on ten other agronomic traits, including plant height, three spike-related traits and six grain-related traits. The compact spike phenotype was correlated with decreased grain size and weight, but with an increase in floret fertility and grain number. These pleiotropic effects make club wheat have compatible spike weight with a normal spike from common wheat. The genetic effects of various gene combinations of C with four yield-related genes, including Ppd-D1, Vrn-D3, Rht-B1b and Rht8, were evaluated. C had no epistatic interaction with any of these genes, indicating that their combinations would have an additive effect on other agronomically important traits. Our research provided a theoretical foundation for the potentially effective deployment of C gene into modern breeding varieties in combination with other favorable alleles.
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10
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The Qc5 Allele Increases Wheat Bread-Making Quality by Regulating SPA and SPR. Int J Mol Sci 2022; 23:ijms23147581. [PMID: 35886927 PMCID: PMC9323144 DOI: 10.3390/ijms23147581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
Common wheat (Triticum aestivum L.) is an important food crop with a unique processing quality. The Q gene positively regulates the processing quality of wheat, but the underlying mechanism remains unclear. Here, a new Q allele (Qc5) responsible for compact spikes and good bread performance was identified. Compared with the Q allele widely distributed in modern common wheat cultivars, Qc5 had a missense mutation outside the miRNA172-binding site. This missense mutation led to a more compact messenger RNA (mRNA) secondary structure around the miRNA172-binding region, resulting in increased Qc5 expression during the spike development stage and a consequent increase in spike density. Furthermore, this missense mutation weakened the physical interaction between Qc5 and storage protein activator (SPA) in seeds and suppressed the expression of storage protein repressor (SPR). These changes increased the grain protein content and improved the bread-making quality of wheat. In conclusion, a missense mutation increases Q expression because of the resulting highly folded mRNA secondary structure around the miRNA172-binding site. Furthermore, this mutation improves the bread-making quality of wheat by repressing the expression of SPR and influencing the physical interaction between Q and SPA. These findings provide new insights into the miRNA172-directed regulation of gene expression, with implications for wheat breeding.
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11
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Zhang X, Qiao L, Li X, Yang Z, Liu C, Guo H, Zheng J, Zhang S, Chang L, Chen F, Jia J, Yan L, Chang Z. Genetic Incorporation of the Favorable Alleles for Three Genes Associated With Spikelet Development in Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:892642. [PMID: 35592560 PMCID: PMC9111956 DOI: 10.3389/fpls.2022.892642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
The number of spikelets per spike is an important trait that directly affects grain yield in wheat. Three quantitative trait loci (QTLs) associated with spikelet nodes per spike (SNS) were mapped in a population of recombinant inbred lines generated from a cross between two advanced breeding lines of winter wheat based on the phenotypic variation evaluated over six locations/years. Two of the three QTLs are QSns.sxau-2A at the WHEATFRIZZY PANICLE (WFZP) loci and QSns.sxau-7A at the WHEAT ORTHOLOG OF APO1 (WAPO1) loci. The WFZP-A1b allele with a 14-bp deletion at QSns.sxau-2A was associated with increased spikelets per spike. WAPO-A1e, as a novel allele at WAPO1, were regulated at the transcript level that was associated with the SNS trait. The third SNS QTL, QSns.sxau-7D on chromosome 7D, was not associated with homoeologous WAPO-D1 or any other genes known to regulate SNS. The favorable alleles for each of WZFP-A1, WAPO-A1, and QSns.sxau-7D are identified and incorporated to increase up to 3.4 spikelets per spike in the RIL lines. Molecular markers for the alleles were developed. This study has advanced our understanding of the genetic basis of natural variation in spikelet development in wheat.
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Affiliation(s)
- Xiaojun Zhang
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Linyi Qiao
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Xin Li
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Zujun Yang
- School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Huijuan Guo
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Shuwei Zhang
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Lifang Chang
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Fang Chen
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Juqing Jia
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Liuling Yan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Zhijian Chang
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
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12
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Shi G, Kariyawasam G, Liu S, Leng Y, Zhong S, Ali S, Moolhuijzen P, Moffat CS, Rasmussen JB, Friesen TL, Faris JD, Liu Z. A Conserved Hypothetical Gene Is Required but Not Sufficient for Ptr ToxC Production in Pyrenophora tritici-repentis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:336-348. [PMID: 35100008 DOI: 10.1094/mpmi-12-21-0299-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The fungus Pyrenophora tritici-repentis causes tan spot, an important foliar disease of wheat worldwide. The fungal pathogen produces three necrotrophic effectors, namely Ptr ToxA, Ptr ToxB, and Ptr ToxC to induce necrosis or chlorosis in wheat. Both Ptr ToxA and Ptr ToxB are proteins, and their encoding genes have been cloned. Ptr ToxC was characterized as a low-molecular weight molecule 20 years ago but the one or more genes controlling its production in P. tritici-repentis are unknown. Here, we report the genetic mapping, molecular cloning, and functional analysis of a fungal gene that is required for Ptr ToxC production. The genetic locus controlling the production of Ptr ToxC, termed ToxC, was mapped to a subtelomeric region using segregating biparental populations, genome sequencing, and association analysis. Additional marker analysis further delimited ToxC to a 173-kb region. The predicted genes in the region were examined for presence/absence polymorphism in different races and isolates leading to the identification of a single candidate gene. Functional validation showed that this gene was required but not sufficient for Ptr ToxC production, thus it is designated as ToxC1. ToxC1 encoded a conserved hypothetical protein likely located on the vacuole membrane. The gene was highly expressed during infection, and only one haplotype was identified among 120 isolates sequenced. Our work suggests that Ptr ToxC is not a protein and is likely produced through a cascade of biosynthetic pathway. The identification of ToxC1 is a major step toward revealing the Ptr ToxC biosynthetic pathway and studying its molecular interactions with host factors.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Gayan Kariyawasam
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Yueqiang Leng
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Shaukat Ali
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University Brookings, SD 57006, U.S.A
| | - Paula Moolhuijzen
- Center for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Caroline S Moffat
- Center for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Jack B Rasmussen
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Timothy L Friesen
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, U.S.A
| | - Justin D Faris
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, U.S.A
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
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13
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Running KLD, Momotaz A, Kariyawasam GK, Zurn JD, Acevedo M, Carter AH, Liu Z, Faris JD. Genomic Analysis and Delineation of the Tan Spot Susceptibility Locus Tsc1 in Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:793925. [PMID: 35401609 PMCID: PMC8984248 DOI: 10.3389/fpls.2022.793925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
The necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) causes the foliar disease tan spot in both bread wheat and durum wheat. Wheat lines carrying the tan spot susceptibility gene Tsc1 are sensitive to the Ptr-produced necrotrophic effector (NE) Ptr ToxC. A compatible interaction results in leaf chlorosis, reducing yield by decreasing the photosynthetic area of leaves. Developing genetically resistant cultivars will effectively reduce disease incidence. Toward that goal, the production of chlorosis in response to inoculation with Ptr ToxC-producing isolates was mapped in two low-resolution biparental populations derived from LMPG-6 × PI 626573 (LP) and Louise × Penawawa (LouPen). In total, 58 genetic markers were developed and mapped, delineating the Tsc1 candidate gene region to a 1.4 centiMorgan (cM) genetic interval spanning 184 kb on the short arm of chromosome 1A. A total of nine candidate genes were identified in the Chinese Spring reference genome, seven with protein domains characteristic of resistance genes. Mapping of the chlorotic phenotype, development of genetic markers, both for genetic mapping and marker-assisted selection (MAS), and the identification of Tsc1 candidate genes provide a foundation for map-based cloning of Tsc1.
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Affiliation(s)
| | - Aliya Momotaz
- USDA-Agricultural Research Service, Sugarcane Field Station, Canal Point, FL, United States
| | - Gayan K. Kariyawasam
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Jason D. Zurn
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Maricelis Acevedo
- Department of Global Development, Cornell University, Ithaca, NY, United States
| | - Arron H. Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Justin D. Faris
- USDA-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
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14
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Improvement and Re-Evolution of Tetraploid Wheat for Global Environmental Challenge and Diversity Consumption Demand. Int J Mol Sci 2022; 23:ijms23042206. [PMID: 35216323 PMCID: PMC8878472 DOI: 10.3390/ijms23042206] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 02/01/2023] Open
Abstract
Allotetraploid durum wheat is the second most widely cultivated wheat, following hexaploid bread wheat, and is one of the major protein and calorie sources of the human diet. However, durum wheat is encountered with a severe grain yield bottleneck due to the erosion of genetic diversity stemming from long-term domestication and especially modern breeding programs. The improvement of yield and grain quality of durum wheat is crucial when confronted with the increasing global population, changing climate environments, and the non-ignorable increasing incidence of wheat-related disorders. This review summarized the domestication and evolution process and discussed the durum wheat re-evolution attempts performed by global researchers using diploid einkorn, tetraploid emmer wheat, hexaploid wheat (particularly the D-subgenome), etc. In addition, the re-evolution of durum wheat would be promoted by the genetic enrichment process, which could diversify allelic combinations through enhancing chromosome recombination (pentaploid hybridization or pairing of homologous chromosomes gene Ph mutant line induced homoeologous recombination) and environmental adaptability via alien introgressive genes (wide cross or distant hybridization followed by embryo rescue), and modifying target genes or traits by molecular approaches, such as CRISPR/Cas9 or RNA interference (RNAi). A brief discussion of the future perspectives for exploring germplasm for the modern improvement and re-evolution of durum wheat is included.
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Arriagada O, Gadaleta A, Marcotuli I, Maccaferri M, Campana M, Reveco S, Alfaro C, Matus I, Schwember AR. A comprehensive meta-QTL analysis for yield-related traits of durum wheat ( Triticum turgidum L. var. durum) grown under different water regimes. FRONTIERS IN PLANT SCIENCE 2022; 13:984269. [PMID: 36147234 PMCID: PMC9486101 DOI: 10.3389/fpls.2022.984269] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/18/2022] [Indexed: 05/13/2023]
Abstract
Abiotic stress strongly affects yield-related traits in durum wheat, in particular drought is one of the main environmental factors that have effect on grain yield and plant architecture. In order to obtain new genotypes well adapted to stress conditions, the highest number of desirable traits needs to be combined in the same genotype. In this context, hundreds of quantitative trait loci (QTL) have been identified for yield-related traits in different genetic backgrounds and environments. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies for the reliability of their location and effects. MQTL analysis is a useful method to dissect the genetic architecture of complex traits, which provide an extensive allelic coverage, a higher mapping resolution and allow the identification of putative molecular markers useful for marker-assisted selection (MAS). In the present study, a complete and comprehensive MQTL analysis was carried out to identify genomic regions associated with grain-yield related traits in durum wheat under different water regimes. A total of 724 QTL on all 14 chromosomes (genomes A and B) were collected for the 19 yield-related traits selected, of which 468 were reported under rainfed conditions, and 256 under irrigated conditions. Out of the 590 QTL projected on the consensus map, 421 were grouped into 76 MQTL associated with yield components under both irrigated and rainfed conditions, 12 genomic regions containing stable MQTL on all chromosomes except 1A, 4A, 5A, and 6B. Candidate genes associated to MQTL were identified and an in-silico expression analysis was carried out for 15 genes selected among those that were differentially expressed under drought. These results can be used to increase durum wheat grain yields under different water regimes and to obtain new genotypes adapted to climate change.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Matteo Campana
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Samantha Reveco
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christian Alfaro
- Centro Regional Rayentue, Instituto de Investigaciones Agropecuarias (INIA), Rengo, Chile
| | - Iván Matus
- Centro Regional Quilamapu, Instituto de Investigaciones Agropecuarias (INIA), Chillán, Chile
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
- *Correspondence: Andrés R. Schwember,
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16
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Alvarez JB. Spanish Spelt Wheat: From an Endangered Genetic Resource to a Trendy Crop. PLANTS (BASEL, SWITZERLAND) 2021; 10:2748. [PMID: 34961216 PMCID: PMC8707452 DOI: 10.3390/plants10122748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/04/2021] [Accepted: 12/09/2021] [Indexed: 05/05/2023]
Abstract
Spelt wheat (Triticum aestivum L. ssp. spelta Thell.) is an ancient wheat that was widely cultivated in the past. This species derived from a cross between emmer wheat (T. turgidum spp. dicoccum Schrank em. Thell.) and Aegilops tauschii Coss. Its main origin was in the Fertile Crescent (Near East), with a secondary center of origin in Europe due to a second hybridization event between emmer and hexaploid wheat. This species has been neglected in most of Europe; however, the desire for more natural foods has driven a revival in interest. Iberian spelt is classified as a geographical group differing to the rest of European spelt. In this review, the particularities, genetic diversity and current situation of Spanish spelt, mainly for quality traits, are discussed.
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Affiliation(s)
- Juan B Alvarez
- Edificio Gregor Mendel, Departamento de Genética, Campus de Rabanales, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Universidad de Córdoba, CeiA3, ES-14071 Córdoba, Spain
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17
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Arif MAR, Shokat S, Plieske J, Ganal M, Lohwasser U, Chesnokov YV, Kocherina NV, Kulwal P, Kumar N, McGuire PE, Sorrells ME, Qualset CO, Börner A. A SNP-based genetic dissection of versatile traits in bread wheat (Triticum aestivum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:960-976. [PMID: 34218494 DOI: 10.1111/tpj.15407] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/14/2021] [Indexed: 05/20/2023]
Abstract
The continuous increase in global population prompts increased wheat production. Future wheat (Triticum aestivum L.) breeding will heavily rely on dissecting molecular and genetic bases of wheat yield and related traits which is possible through the discovery of quantitative trait loci (QTLs) in constructed populations, such as recombinant inbred lines (RILs). Here, we present an evaluation of 92 RILs in a bi-parental RIL mapping population (the International Triticeae Mapping Initiative Mapping Population [ITMI/MP]) using newly generated phenotypic data in 3-year experiments (2015), older phenotypic data (1997-2009), and newly created single nucleotide polymorphism (SNP) marker data based on 92 of the original RILs to search for novel and stable QTLs. Our analyses of more than 15 unique traits observed in multiple experiments included analyses of 46 traits in three environments in the USA, 69 traits in eight environments in Germany, 149 traits in 10 environments in Russia, and 28 traits in four environments in India (292 traits in 25 environments) with 7584 SNPs (292 × 7584 = 2 214 528 data points). A total of 874 QTLs were detected with limit of detection (LOD) scores of 2.01-3.0 and 432 QTLs were detected with LOD > 3.0. Moreover, 769 QTLs could be assigned to 183 clusters based on the common markers and relative proximity of related QTLs, indicating gene-rich regions throughout the A, B, and D genomes of common wheat. This upgraded genotype-phenotype information of ITMI/MP can assist breeders and geneticists who can make crosses with suitable RILs to improve or investigate traits of interest.
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Affiliation(s)
- Mian Abdur Rehman Arif
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | - Sajid Shokat
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | - Jörg Plieske
- SGS Institut Fresenius GmbH TraitGenetics Section, Am Schwabeplan 1b, Stadt Seeland, OT Gatersleben, 06466, Germany
| | - Martin Ganal
- SGS Institut Fresenius GmbH TraitGenetics Section, Am Schwabeplan 1b, Stadt Seeland, OT Gatersleben, 06466, Germany
| | - Ulrike Lohwasser
- Resources Genetics and Reproduction Group, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Seeland, OT Gatersleben, 06466, Germany
| | - Yuriy V Chesnokov
- Laboratory of Ecological Genetics and Plant Breeding, Agrophysical Research Institute, Grazhdanskiy pr. 14, St. Petersburg, 195220, Russia
| | - Nataliya V Kocherina
- Laboratory of Ecological Genetics and Plant Breeding, Agrophysical Research Institute, Grazhdanskiy pr. 14, St. Petersburg, 195220, Russia
| | - Pawan Kulwal
- State Level Biotechnology Centre, Mahatma Phule Krishi Vidyapeeth, Rahuri, Ahmednagar, Maharashtra, 413 722, India
| | - Neeraj Kumar
- Department of Plant and Environmental Sciences, Clemson University, 100C Biosystems Research Complex 105 Collings Street, Clemson, SC, 29634-0141, USA
| | - Patrick E McGuire
- Plant Sciences Department, University of California, Mail Stop 3, One Shields Avenue, Davis, CA, 95616, USA
| | - Mark E Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Calvin O Qualset
- Plant Sciences Department, University of California, Mail Stop 3, One Shields Avenue, Davis, CA, 95616, USA
| | - Andreas Börner
- Resources Genetics and Reproduction Group, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Seeland, OT Gatersleben, 06466, Germany
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18
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Colasuonno P, Marcotuli I, Gadaleta A, Soriano JM. From Genetic Maps to QTL Cloning: An Overview for Durum Wheat. PLANTS (BASEL, SWITZERLAND) 2021; 10:315. [PMID: 33562160 PMCID: PMC7914919 DOI: 10.3390/plants10020315] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 12/17/2022]
Abstract
Durum wheat is one of the most important cultivated cereal crops, providing nutrients to humans and domestic animals. Durum breeding programs prioritize the improvement of its main agronomic traits; however, the majority of these traits involve complex characteristics with a quantitative inheritance (quantitative trait loci, QTL). This can be solved with the use of genetic maps, new molecular markers, phenotyping data of segregating populations, and increased accessibility to sequences from next-generation sequencing (NGS) technologies. This allows for high-density genetic maps to be developed for localizing candidate loci within a few Kb in a complex genome, such as durum wheat. Here, we review the identified QTL, fine mapping, and cloning of QTL or candidate genes involved in the main traits regarding the quality and biotic and abiotic stresses of durum wheat. The current knowledge on the used molecular markers, sequence data, and how they changed the development of genetic maps and the characterization of QTL is summarized. A deeper understanding of the trait architecture useful in accelerating durum wheat breeding programs is envisioned.
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Affiliation(s)
- Pasqualina Colasuonno
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Jose Miguel Soriano
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198 Lleida, Spain
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19
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Mo Z, Zhu J, Wei J, Zhou J, Xu Q, Tang H, Mu Y, Deng M, Jiang Q, Liu Y, Chen G, Wang J, Qi P, Li W, Wei Y, Zheng Y, Lan X, Ma J. The 55K SNP-Based Exploration of QTLs for Spikelet Number Per Spike in a Tetraploid Wheat ( Triticum turgidum L.) Population: Chinese Landrace "Ailanmai" × Wild Emmer. FRONTIERS IN PLANT SCIENCE 2021; 12:732837. [PMID: 34531890 PMCID: PMC8439258 DOI: 10.3389/fpls.2021.732837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/18/2021] [Indexed: 05/08/2023]
Abstract
Spikelet number per spike (SNS) is the primary factor that determines wheat yield. Common wheat breeding reduces the genetic diversity among elite germplasm resources, leading to a detrimental effect on future wheat production. It is, therefore, necessary to explore new genetic resources for SNS to increase wheat yield. A tetraploid landrace "Ailanmai" × wild emmer wheat recombinant inbred line (RIL) population was used to construct a genetic map using a wheat 55K single- nucleotide polymorphism (SNP) array. The linkage map containing 1,150 bin markers with a total genetic distance of 2,411.8 cm was obtained. Based on the phenotypic data from the eight environments and best linear unbiased prediction (BLUP) values, five quantitative trait loci (QTLs) for SNS were identified, explaining 6.71-29.40% of the phenotypic variation. Two of them, QSns.sau-AM-2B.2 and QSns.sau-AM-3B.2, were detected as a major and novel QTL. Their effects were further validated in two additional F2 populations using tightly linked kompetitive allele-specific PCR (KASP) markers. Potential candidate genes within the physical intervals of the corresponding QTLs were predicted to participate in inflorescence development and spikelet formation. Genetic associations between SNS and other agronomic traits were also detected and analyzed. This study demonstrates the feasibility of the wheat 55K SNP array developed for common wheat in the genetic mapping of tetraploid population and shows the potential application of wheat-related species in wheat improvement programs.
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Affiliation(s)
- Ziqiang Mo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jing Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiatai Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Xiujin Lan
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Jian Ma
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20
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Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative. G3-GENES GENOMES GENETICS 2020; 10:3651-3661. [PMID: 32737066 PMCID: PMC7534432 DOI: 10.1534/g3.120.401479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Introgression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. Overall, introgression frequency positively correlated with recombination rate, with a high incidence of introgression at the ends of chromosomes and low in the pericentromeric regions, and was negatively related to sequence divergence between the parental genomes. Reduced introgression in the pericentromeric low-recombining regions spans nearly 2/3 of each chromosome arm, suggestive of the polygenic nature of introgression barriers that could be associated with multilocus negative epistasis between the alleles of wild and cultivated wheat. On the contrary, negative selection against the wild allele of Tg, controlling free-threshing trait and located in the high-recombining chromosomal region, led to reduced introgression only within ∼10 Mbp region around Tg. These results are consistent with the effect of selection on linked variation described by the Hill-Robertson effect, and offer insights into the introgression population development for crop improvement to maximize retention of introgressed diversity across entire genome.
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21
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Arriagada O, Marcotuli I, Gadaleta A, Schwember AR. Molecular Mapping and Genomics of Grain Yield in Durum Wheat: A Review. Int J Mol Sci 2020; 21:ijms21197021. [PMID: 32987666 PMCID: PMC7582296 DOI: 10.3390/ijms21197021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
Durum wheat is the most relevant cereal for the whole of Mediterranean agriculture, due to its intrinsic adaptation to dryland and semi-arid environments and to its strong historical cultivation tradition. It is not only relevant for the primary production sector, but also for the food industry chains associated with it. In Mediterranean environments, wheat is mostly grown under rainfed conditions and the crop is frequently exposed to environmental stresses, with high temperatures and water scarcity especially during the grain filling period. For these reasons, and due to recurrent disease epidemics, Mediterranean wheat productivity often remains under potential levels. Many studies, using both linkage analysis (LA) and a genome-wide association study (GWAS), have identified the genomic regions controlling the grain yield and the associated markers that can be used for marker-assisted selection (MAS) programs. Here, we have summarized all the current studies identifying quantitative trait loci (QTLs) and/or candidate genes involved in the main traits linked to grain yield: kernel weight, number of kernels per spike and number of spikes per unit area.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, 306-22 Santiago, Chile;
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70121 Bari, Italy; (I.M.); (A.G.)
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70121 Bari, Italy; (I.M.); (A.G.)
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, 306-22 Santiago, Chile;
- Correspondence: ; Tel.: +56-223544123
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Faris JD, Overlander ME, Kariyawasam GK, Carter A, Xu SS, Liu Z. Identification of a major dominant gene for race-nonspecific tan spot resistance in wild emmer wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:829-841. [PMID: 31863156 DOI: 10.1007/s00122-019-03509-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
A single dominant gene found in tetraploid and hexaploid wheat controls broad-spectrum race-nonspecific resistance to the foliar disease tan spot caused by Pyrenophora tritici-repentis. Tan spot is an important foliar disease of durum and common wheat caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis. Genetic studies in common wheat have shown that pathogen-produced necrotrophic effectors interact with host genes in an inverse gene-for-gene manner to cause disease, but quantitative trait loci (QTLs) with broad race-nonspecific resistance also exist. Less work has been done to understand the genetics of tan spot interactions in durum wheat. Here, we evaluated a set of Langdon durum-wild emmer (Triticum turgidum ssp. dicoccoides) disomic chromosome substitution lines for reaction to four P. tritici-repentis isolates representing races 1, 2, 3, and 5 to identify wild emmer chromosomes potentially containing tan spot resistance genes. Chromosome 3B from the wild emmer accession IsraelA rendered the tan spot-susceptible durum cultivar Langdon resistant to all four fungal isolates. Genetic analysis indicated that a single dominant gene, designated Tsr7, governed resistance. Detailed mapping experiments showed that the Tsr7 locus is likely the same as the race-nonspecific QTL previously identified in the hexaploid wheat cultivars BR34 and Penawawa. Four user-friendly SNP-based semi-thermal asymmetric reverse PCR (STARP) markers cosegregated with Tsr7 and should be useful for marker-assisted selection of resistance. In addition to 3B, other wild emmer chromosomes contributed moderate levels of tan spot resistance, and, as has been shown previously for tetraploid wheat, the Tsn1-Ptr ToxA interaction was not associated with susceptibility. This is the first report of a major dominant gene governing resistance to tan spot in tetraploid wheat.
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Affiliation(s)
- Justin D Faris
- Northern Crop Science Laboratory, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-Agricultural Research Service, 1616 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA.
| | - Megan E Overlander
- Northern Crop Science Laboratory, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-Agricultural Research Service, 1616 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA
| | - Gayan K Kariyawasam
- Department of Plant Pathology, North Dakota State University, 306 Walster Hall, Fargo, ND, 58105, USA
| | - Arron Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Steven S Xu
- Northern Crop Science Laboratory, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-Agricultural Research Service, 1616 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, 306 Walster Hall, Fargo, ND, 58105, USA.
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Sun L, Huang S, Sun G, Zhang Y, Hu X, Nevo E, Peng J, Sun D. SNP-based association study of kernel architecture in a worldwide collection of durum wheat germplasm. PLoS One 2020; 15:e0229159. [PMID: 32059028 PMCID: PMC7021289 DOI: 10.1371/journal.pone.0229159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 01/30/2020] [Indexed: 12/25/2022] Open
Abstract
Durum wheat, genetic resource with favorable alleles is considered as natural gene pool for wheat breeding. Kernel size and weight are important factors affecting grain yield in crops. Here, association analysis was performed to dissect the genetic constitution of kernel-related traits in 150 lines collected from 46 countries and regions using a set of EST-derived and genome-wide SNP markers with five consecutive years of data. Total 109 significant associations for eight kernel-related traits were detected under a mix linear model, generating 54 unique SNP markers distributed on 13 of 14 chromosomes. Of which, 19 marker-trait associations were identified in two or more environments, including one stable and pleiotropic SNP BE500291_5_A_37 on chromosome 5A correlated with six kernel traits. Although most of our SNP loci were overlapped with the previously known kernel weight QTLs, several novel loci for kernel traits in durum were reported. Correlation analysis implied that the moderate climatic variables during growth and development of durum are needed for the large grain size and high grain weight. Combined with our previous studies, we found that chromosome 5A might play an important role in durum growth and development.
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Affiliation(s)
- Longqing Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Sisi Huang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Genlou Sun
- Biology Department, Saint Mary’s University, Halifax, Nova Scotia, Canada
| | - Yujuan Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xin Hu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, Israel
| | - Junhua Peng
- Germplasm Enhancement Department, Huazhi Biotech Institute, Changsa, Hunan, China
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, Hubei, China
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Kuzay S, Xu Y, Zhang J, Katz A, Pearce S, Su Z, Fraser M, Anderson JA, Brown-Guedira G, DeWitt N, Peters Haugrud A, Faris JD, Akhunov E, Bai G, Dubcovsky J. Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2689-2705. [PMID: 31254024 PMCID: PMC6708044 DOI: 10.1007/s00122-019-03382-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/12/2019] [Accepted: 06/16/2019] [Indexed: 05/21/2023]
Abstract
A high-resolution genetic map combined with haplotype analyses identified a wheat ortholog of rice gene APO1 as the best candidate gene for a 7AL locus affecting spikelet number per spike. A better understanding of the genes controlling differences in wheat grain yield components can accelerate the improvements required to satisfy future food demands. In this study, we identified a promising candidate gene underlying a quantitative trait locus (QTL) on wheat chromosome arm 7AL regulating spikelet number per spike (SNS). We used large heterogeneous inbred families ( > 10,000 plants) from two crosses to map the 7AL QTL to an 87-kb region (674,019,191-674,106,327 bp, RefSeq v1.0) containing two complete and two partial genes. In this region, we found three major haplotypes that were designated as H1, H2 and H3. The H2 haplotype contributed the high-SNS allele in both H1 × H2 and H2 × H3 segregating populations. The ancestral H3 haplotype is frequent in wild emmer (48%) but rare (~ 1%) in cultivated wheats. By contrast, the H1 and H2 haplotypes became predominant in modern cultivated durum and common wheat, respectively. Among the four candidate genes, only TraesCS7A02G481600 showed a non-synonymous polymorphism that differentiated H2 from the other two haplotypes. This gene, designated here as WHEAT ORTHOLOG OF APO1 (WAPO1), is an ortholog of the rice gene ABERRANT PANICLE ORGANIZATION 1 (APO1), which affects spikelet number. Taken together, the high-resolution genetic map, the association between polymorphisms in the different mapping populations with differences in SNS, and the known role of orthologous genes in other grass species suggest that WAPO-A1 is the most likely candidate gene for the 7AL SNS QTL among the four genes identified in the candidate gene region.
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Affiliation(s)
- Saarah Kuzay
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yunfeng Xu
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Junli Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Andrew Katz
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Zhenqi Su
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Max Fraser
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Noah DeWitt
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Justin D Faris
- USDA-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA.
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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25
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Yao H, Xie Q, Xue S, Luo J, Lu J, Kong Z, Wang Y, Zhai W, Lu N, Wei R, Yang Y, Han Y, Zhang Y, Jia H, Ma Z. HL2 on chromosome 7D of wheat (Triticum aestivum L.) regulates both head length and spikelet number. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1789-1797. [PMID: 30810762 DOI: 10.1007/s00122-019-03315-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/15/2019] [Indexed: 05/24/2023]
Abstract
A major QTL QSpl.nau-7D, named HL2, was validated for its effects on head length and kernel number per spike using NIL, and mapped to a 0.2 cM interval using recombinants. Improvement in wheat inflorescence traits such as spike or head length and spikelet number provides an important avenue to increase grain yield potential. In a previous study, QSpl.nau-7D, the major QTL for head length on chromosome 7D, was identified in the recombinant inbred lines derived from Nanda2419 and Wangshuibai. To validate and precisely map this QTL, the Wangshuibai allele was transferred to elite cultivar Yangmai15 through marker-assisted selection. Compared with the recurrent parent, the resultant near-isogenic line (NIL) yielded not only 28% longer spikes on the average but also more spikelets and kernels per spike. Moreover, the NIL had a lower spikelet density and did not show significant kernel weight change. In the F2 population derived from the NIL, QSpl.nau-7D acted like a single semi-dominant gene controlling head length and was therefore designated as Head Length 2 (HL2). With this population, a high-density genetic map was constructed mainly using newly developed markers, and 100 homozygous recombinants including 17 genotypes were obtained. Field experiments showed that the recombinants carrying the 0.2-cM interval flanked by Xwgrb1588 and Xwgrb1902 from Wangshuibai produced longer spikes than those without this Wangshuibai allele. Comparative mapping of this interval revealed a conserved synteny among cereal grasses. HL2 is beneficial to wheat breeding for more kernels per spike at a lower spikelet density, which is a favored morphological trait for Fusarium head blight resistance.
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Affiliation(s)
- Hongni Yao
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Quan Xie
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Shulin Xue
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Jing Luo
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jikang Lu
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhongxin Kong
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yongpan Wang
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Wenling Zhai
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Nan Lu
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Rong Wei
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yang Yang
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yuzhou Han
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yong Zhang
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Haiyan Jia
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhengqiang Ma
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
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Desiderio F, Zarei L, Licciardello S, Cheghamirza K, Farshadfar E, Virzi N, Sciacca F, Bagnaresi P, Battaglia R, Guerra D, Palumbo M, Cattivelli L, Mazzucotelli E. Genomic Regions From an Iranian Landrace Increase Kernel Size in Durum Wheat. FRONTIERS IN PLANT SCIENCE 2019; 10:448. [PMID: 31057571 PMCID: PMC6482228 DOI: 10.3389/fpls.2019.00448] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/25/2019] [Indexed: 05/27/2023]
Abstract
Kernel size and shape are important parameters determining the wheat profitability, being main determinants of yield and its technological quality. In this study, a segregating population of 118 recombinant inbred lines, derived from a cross between the Iranian durum landrace accession "Iran_249" and the Iranian durum cultivar "Zardak", was used to investigate durum wheat kernel morphology factors and their relationships with kernel weight, and to map the corresponding QTLs. A high density genetic map, based on wheat 90k iSelect Infinium SNP assay, comprising 6,195 markers, was developed and used to perform the QTL analysis for kernel length and width, traits related to kernel shape and weight, and heading date, using phenotypic data from three environments. Overall, a total of 31 different QTLs and 9 QTL interactions for kernel size, and 21 different QTLs and 5 QTL interactions for kernel shape were identified. The landrace Iran_249 contributed the allele with positive effect for most of the QTLs related to kernel length and kernel weight suggesting that the landrace might have considerable potential toward enhancing the existing gene pool for grain shape and size traits and for further yield improvement in wheat. The correlation among traits and co-localization of corresponding QTLs permitted to define 11 clusters suggesting causal relationships between simplest kernel size trait, like kernel length and width, and more complex secondary trait, like kernel shape and weight related traits. Lastly, the recent release of the T. durum reference genome sequence allowed to define the physical interval of our QTL/clusters and to hypothesize novel candidate genes inspecting the gene content of the genomic regions associated to target traits.
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Affiliation(s)
- Francesca Desiderio
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Leila Zarei
- Department of Agronomy and Plant Breeding, Razi University, Kermanshah, Iran
| | - Stefania Licciardello
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | | | | | - Nino Virzi
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | - Fabiola Sciacca
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Raffaella Battaglia
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Davide Guerra
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Massimo Palumbo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
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Vendramin V, Ormanbekova D, Scalabrin S, Scaglione D, Maccaferri M, Martelli P, Salvi S, Jurman I, Casadio R, Cattonaro F, Tuberosa R, Massi A, Morgante M. Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm. BMC Genomics 2019; 20:278. [PMID: 30971220 PMCID: PMC6456968 DOI: 10.1186/s12864-019-5645-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 03/25/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The tetraploid durum wheat (Triticum turgidum L. ssp. durum Desf. Husnot) is an important crop which provides the raw material for pasta production and a valuable source of genetic diversity for breeding hexaploid wheat (Triticum aestivum L.). Future breeding efforts to enhance yield potential and climate resilience will increasingly rely on genomics-based approaches to identify and select beneficial alleles. A deeper characterisation of the molecular and functional diversity of the durum wheat transcriptome will be instrumental to more effectively harness its genetic diversity. RESULTS We report on the de novo transcriptome assembly of durum wheat cultivar 'Svevo'. The transcriptome of four tissues/organs (shoots and roots at the seedling stage, reproductive organs and developing grains) was assembled de novo, yielding 180,108 contigs, with a N50 length of 1121 bp and mean contig length of 883 bp. Alignment against the transcriptome of nine plant species identified 43% of transcripts with homology to at least one reference transcriptome. The functional annotation was completed by means of a combination of complementary software. The presence of differential expression between the A- and B-homoeolog copies of the durum wheat tetraploid genome was ascertained by phase reconstruction of polymorphic sites based on the T. urartu transcripts and inferring homoeolog-specific sequences. We observed greater expression divergence between A and B homoeologs in grains rather than in leaves and roots. The transcriptomes of 13 durum wheat cultivars spanning the breeding period from 1969 to 2005 were analysed for SNP diversity, leading to 95,358 non-rare, hemi-SNPs shared among two or more cultivars and 33,747 locus-specific (diploid inheritance) SNPs. CONCLUSIONS Our study updates and expands the de novo transcriptome reference assembly available for durum wheat. Out of 180,108 assembled transcripts, 13,636 were specific to the Svevo cultivar as compared to the only other reference transcriptome available for durum, thus contributing to the identification of the tetraploid wheat pan-transcriptome. Additionally, the analysis of 13 historically relevant hallmark varieties produced a SNP dataset that could successfully validate the genotyping in tetraploid wheat and provide a valuable resource for genomics-assisted breeding of both tetraploid and hexaploid wheats.
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Affiliation(s)
- Vera Vendramin
- IGA Technology Services, via J. Linussio 51, 33100, Udine, Italy.
| | - Danara Ormanbekova
- Department of Agricultural and Food Sciences DISTAL, University of Bologna, Viale G. Fanin 44, 40127, Bologna, Italy
| | - Simone Scalabrin
- IGA Technology Services, via J. Linussio 51, 33100, Udine, Italy
| | - Davide Scaglione
- IGA Technology Services, via J. Linussio 51, 33100, Udine, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences DISTAL, University of Bologna, Viale G. Fanin 44, 40127, Bologna, Italy
| | - Pierluigi Martelli
- Biocomputing Group, University of Bologna, via San Giacomo 9/2, 40126, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural and Food Sciences DISTAL, University of Bologna, Viale G. Fanin 44, 40127, Bologna, Italy
| | - Irena Jurman
- Istituto di Genomica Applicata, via J. Linussio 51, 33100, Udine, Italy
| | - Rita Casadio
- Biocomputing Group, University of Bologna, via San Giacomo 9/2, 40126, Bologna, Italy
| | | | - Roberto Tuberosa
- Department of Agricultural and Food Sciences DISTAL, University of Bologna, Viale G. Fanin 44, 40127, Bologna, Italy
| | - Andrea Massi
- Società produttori Sementi Bologna, Via Macero 1, 40050, Argelato, BO, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata, via J. Linussio 51, 33100, Udine, Italy.,Department od Agricultural, Food, Environmental and Animal Research - DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy
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28
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Sharma JS, Running KLD, Xu SS, Zhang Q, Peters Haugrud AR, Sharma S, McClean PE, Faris JD. Genetic analysis of threshability and other spike traits in the evolution of cultivated emmer to fully domesticated durum wheat. Mol Genet Genomics 2019; 294:757-771. [PMID: 30887143 DOI: 10.1007/s00438-019-01544-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/27/2019] [Indexed: 12/11/2022]
Abstract
Genetic mutations in genes governing wheat threshability were critical for domestication. Knowing when these genes mutated during wheat evolution will provide more insight into the domestication process and lead to further exploitation of primitive alleles for wheat improvement. We evaluated a population of recombinant inbred lines derived from a cross between the durum variety Rusty and the cultivated emmer accession PI 193883 for threshability, rachis fragility, and other spike-related traits. Quantitative trait loci (QTL) associated with spike length, spikelets per spike, and spike compactness were primarily associated with known genes such as the pleiotropic domestication gene Q. Interestingly, rachis fragility was not associated with the Q locus, suggesting that this trait, usually a pleiotropic effect of the q allele, can be influenced by the genetic background. Threshability QTL were identified on chromosome arms 2AS, 2BS, and 5AL corresponding to the tenacious glume genes Tg2A and Tg2B as well as the Q gene, respectively, further demonstrating that cultivated emmer harbors the primitive non-free-threshing alleles at all three loci. Genetic analysis indicated that the effects of the three genes are mostly additive, with Q having the most profound effects on threshability, and that free-threshing alleles are necessary at all three loci to attain a completely free-threshing phenotype. These findings provide further insight into the timeline and possible pathways of wheat domestication and evolution that led to the formation of modern day domesticated wheats.
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Affiliation(s)
- Jyoti S Sharma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB, R6M 1Y5, Canada
| | | | - Steven S Xu
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Northern Crop Science Laboratory, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA
| | - Qijun Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | | | - Sapna Sharma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Phillip E McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Justin D Faris
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Northern Crop Science Laboratory, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA.
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29
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Song G, Sun G, Kong X, Jia M, Wang K, Ye X, Zhou Y, Geng S, Mao L, Li A. The soft glumes of common wheat are sterile-lemmas as determined by the domestication gene Q. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2018.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Genotype Imputation in Winter Wheat Using First-Generation Haplotype Map SNPs Improves Genome-Wide Association Mapping and Genomic Prediction of Traits. G3-GENES GENOMES GENETICS 2019; 9:125-133. [PMID: 30420469 PMCID: PMC6325902 DOI: 10.1534/g3.118.200664] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Genome-wide single nucleotide polymorphism (SNP) variation allows for the capture of haplotype structure in populations and prediction of unobserved genotypes based on inferred regions of identity-by-descent (IBD). Here we have used a first-generation wheat haplotype map created by targeted re-sequencing of low-copy genomic regions in the reference panel of 62 lines to impute marker genotypes in a diverse panel of winter wheat cultivars from the U.S. Great Plains. The IBD segments between the reference population and winter wheat cultivars were identified based on SNP genotyped using the 90K iSelect wheat array and genotyping by sequencing (GBS). A genome-wide association study and genomic prediction of resistance to stripe rust in winter wheat cultivars showed that an increase in marker density achieved by imputation improved both the power and precision of trait mapping and prediction. The majority of the most significant marker-trait associations belonged to imputed genotypes. With the vast amount of SNP variation data accumulated for wheat in recent years, the presented imputation framework will greatly improve prediction accuracy in breeding populations and increase resolution of trait mapping hence, facilitate cross-referencing of genotype datasets available across different wheat populations.
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Avni R, Oren L, Shabtay G, Assili S, Pozniak C, Hale I, Ben-David R, Peleg Z, Distelfeld A. Genome Based Meta-QTL Analysis of Grain Weight in Tetraploid Wheat Identifies Rare Alleles of GRF4 Associated with Larger Grains. Genes (Basel) 2018; 9:genes9120636. [PMID: 30562998 PMCID: PMC6315823 DOI: 10.3390/genes9120636] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/11/2018] [Accepted: 12/11/2018] [Indexed: 12/12/2022] Open
Abstract
The domestication and subsequent genetic improvement of wheat led to the development of large-seeded cultivated wheat species relative to their smaller-seeded wild progenitors. While increased grain weight (GW) continues to be an important goal of many wheat breeding programs, few genes underlying this trait have been identified despite an abundance of studies reporting quantitative trait loci (QTL) for GW. Here we perform a QTL analysis for GW using a population of recombinant inbred lines (RILs) derived from the cross between wild emmer wheat accession ‘Zavitan’ and durum wheat variety ‘Svevo’. Identified QTLs in this population were anchored to the recent Zavitan reference genome, along with previously published QTLs for GW in tetraploid wheat. This genome-based, meta-QTL analysis enabled the identification of a locus on chromosome 6A whose introgression from wild wheat positively affects GW. The locus was validated using an introgression line carrying the 6A GW QTL region from Zavitan in a Svevo background, resulting in >8% increase in GW compared to Svevo. Using the reference sequence for the 6A QTL region, we identified a wheat ortholog to OsGRF4, a rice gene previously associated with GW. The coding sequence of this gene (TtGRF4-A) contains four single nucleotide polymorphisms (SNPs) between Zavitan and Svevo, one of which reveals the Zavitan allele to be rare in a core collection of wild emmer and completely absent from the domesticated emmer genepool. Similarly, another wild emmer accession (G18-16) was found to carry a rare allele of TtGRF4-A that also positively affects GW and is characterized by a unique SNP absent from the entire core collection. These results exemplify the rich genetic diversity of wild wheat, posit TtGRF4-A as a candidate gene underlying the 6A GW QTL, and suggest that the natural Zavitan and G18-16 alleles of TtGRF4-A have potential to increase wheat yields in breeding programs.
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Affiliation(s)
- Raz Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Leah Oren
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 6997801, Israel.
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel.
| | - Gai Shabtay
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Siwar Assili
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel.
- The Institute of Plant Sciences, Agriculture Research Organization (ARO)-Volcani, Rishon LeZion 7505101, Israel.
| | - Curtis Pozniak
- University of Saskatchewan, Saskatoon SK S7N 5A8, Canada.
| | - Iago Hale
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, USA.
| | - Roi Ben-David
- The Institute of Plant Sciences, Agriculture Research Organization (ARO)-Volcani, Rishon LeZion 7505101, Israel.
| | - Zvi Peleg
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel.
| | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 6997801, Israel.
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Liu W, Maccaferri M, Chen X, Laghetti G, Pignone D, Pumphrey M, Tuberosa R. Genome-wide association mapping reveals a rich genetic architecture of stripe rust resistance loci in emmer wheat (Triticum turgidum ssp. dicoccum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2249-2270. [PMID: 28770301 PMCID: PMC5641275 DOI: 10.1007/s00122-017-2957-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/26/2017] [Indexed: 05/05/2023]
Abstract
KEY MESSAGE SNP-based genome scanning in worldwide domesticated emmer germplasm showed high genetic diversity, rapid linkage disequilibrium decay and 51 loci for stripe rust resistance, a large proportion of which were novel. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum), one of the oldest domesticated crops in the world, is a potentially rich reservoir of variation for improvement of resistance/tolerance to biotic and abiotic stresses in wheat. Resistance to stripe rust (Puccinia striiformis f. sp. tritici) in emmer wheat has been under-investigated. Here, we employed genome-wide association (GWAS) mapping with a mixed linear model to dissect effective stripe rust resistance loci in a worldwide collection of 176 cultivated emmer wheat accessions. Adult plants were tested in six environments and seedlings were evaluated with five races from the United States and one from Italy under greenhouse conditions. Five accessions were resistant across all experiments. The panel was genotyped with the wheat 90,000 Illumina iSelect single nucleotide polymorphism (SNP) array and 5106 polymorphic SNP markers with mapped positions were obtained. A high level of genetic diversity and fast linkage disequilibrium decay were observed. In total, we identified 14 loci associated with field resistance in multiple environments. Thirty-seven loci were significantly associated with all-stage (seedling) resistance and six of them were effective against multiple races. Of the 51 total loci, 29 were mapped distantly from previously reported stripe rust resistance genes or quantitative trait loci and represent newly discovered resistance loci. Our results suggest that GWAS is an effective method for characterizing genes in cultivated emmer wheat and confirm that emmer wheat is a rich source of stripe rust resistance loci that can be used for wheat improvement.
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Affiliation(s)
- Weizhen Liu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Marco Maccaferri
- Department of Agricultural Sciences, University of Bologna, 40127, Bologna, Italy
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, USDA-ARS, Pullman, WA, 99164-6430, USA
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Gaetano Laghetti
- CNR-Institute of Biosciences and Bioresources, 072006, Bari, Italy
| | - Domenico Pignone
- CNR-Institute of Biosciences and Bioresources, 072006, Bari, Italy
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, 40127, Bologna, Italy
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Debernardi JM, Lin H, Chuck G, Faris JD, Dubcovsky J. microRNA172 plays a crucial role in wheat spike morphogenesis and grain threshability. Development 2017; 144:1966-1975. [PMID: 28455375 PMCID: PMC5482987 DOI: 10.1242/dev.146399] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 04/18/2017] [Indexed: 12/12/2022]
Abstract
Wheat domestication from wild species involved mutations in the Q gene. The q allele (wild wheats) is associated with elongated spikes and hulled grains, whereas the mutant Q allele (domesticated wheats) confers subcompact spikes and free-threshing grains. Previous studies showed that Q encodes an AP2-like transcription factor, but the causal polymorphism of the domestication traits remained unclear. Here, we show that the interaction between microRNA172 (miR172) and the Q allele is reduced by a single nucleotide polymorphism in the miRNA binding site. Inhibition of miR172 activity by a miRNA target mimic resulted in compact spikes and transition from glumes to florets in apical spikelets. By contrast, overexpression of miR172 was sufficient to induce elongated spikes and non-free-threshing grains, similar to those observed in three Q loss-of-function mutations. These lines showed transitions from florets to glumes in the basal spikelets. These localized homeotic changes were associated with opposing miR172/Q gradients along the spike. We propose that the selection of a nucleotide change at the miR172 binding site of Q contributed to subcompact spikes and free-threshing grains during wheat domestication. Highlighted Article: A nucleotide change in the microRNA172 binding site of the AP2 gene Q played a critical role in wheat domestication and the origin of free-threshing modern wheats. See also Greenwood et al. in this issue.
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Affiliation(s)
| | - Huiqiong Lin
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - George Chuck
- Plant Gene Expression Center, University of California, Berkeley, Albany, CA 94710, USA
| | - Justin D Faris
- USDA-ARS Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, ND 58102, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA 95616, USA .,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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Gao L, Zhao G, Huang D, Jia J. Candidate loci involved in domestication and improvement detected by a published 90K wheat SNP array. Sci Rep 2017; 7:44530. [PMID: 28327671 PMCID: PMC5361097 DOI: 10.1038/srep44530] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 02/10/2017] [Indexed: 11/12/2022] Open
Abstract
Selection is one of the most important forces in crop evolution. Common wheat is a major world food crop and a typical allopolyploid with a huge and complex genome. We applied four approaches to detect loci selected in wheat during domestication and improvement. A total of 7,984 candidate loci were detected, accounting for 23.3% of all 34,317 SNPs analysed, a much higher proportion than estimated in previous reports. We constructed a first generation wheat selection map which revealed the following new insights on genome-wide selection: (1) diversifying selection acted by increasing, decreasing or not affecting gene frequencies; (2) the number of loci under selection during domestication was much higher than that during improvement; (3) the contribution to wheat improvement by the D sub-genome was relatively small due to the bottleneck of hexaploidisation and diversity can be expanded by using synthetic wheat and introgression lines; and (4) clustered selection regions occur throughout the wheat genome, including the centromere regions. This study will not only help future wheat breeding and evolutionary studies, but will also accelerate study of other crops, especially polyploids.
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Affiliation(s)
- Lifeng Gao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing, 100081, China
| | - Guangyao Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing, 100081, China
| | - Dawei Huang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jizeng Jia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing, 100081, China
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Kariyawasam GK, Carter AH, Rasmussen JB, Faris J, Xu SS, Mergoum M, Liu Z. Genetic relationships between race-nonspecific and race-specific interactions in the wheat-Pyrenophora tritici-repentis pathosystem. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:897-908. [PMID: 26796533 DOI: 10.1007/s00122-016-2670-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/09/2016] [Indexed: 05/15/2023]
Abstract
We identified a major QTL conferring race-nonspecific resistance and revealed its relationships with race-specific interactions in the wheat- Pyrenophora tritici-repentis pathosystem. Tan spot, caused by the fungus Pyrenophora tritici-repentis (Ptr), is a destructive disease of wheat worldwide. The disease system is known to include inverse gene-for-gene, race-specific interactions involving the recognition of fungal-produced necrotrophic effectors (NEs) by corresponding host sensitivity genes. However, quantitative trait loci (QTLs) conferring race-nonspecific resistance have also been identified. In this work, we identified a major race-nonspecific resistance QTL and characterized its genetic relationships with the NE-host gene interactions Ptr ToxA-Tsn1 and Ptr ToxC-Tsc1 in a recombinant inbred wheat population derived from the cross between 'Louise' and 'Penawawa.' Both parental lines were sensitive to Ptr ToxA, but Penawawa and Louise were highly resistant and susceptible, respectively, to conidial inoculations of all races. Resistance was predominantly governed by a major race-nonspecific QTL on chromosome arm 3BL for resistance to all races. Another significant QTL was detected at the distal end of chromosome arm 1AS for resistance to the Ptr ToxC-producing isolates, which corresponded to the known location of the Tsc1 locus. The effects of the 3B and 1A QTLs were largely additive, and the 3B resistance QTL was epistatic to the Ptr ToxA-Tsn1 interaction. Resistance to race 2 in F1 plants was completely dominant; however, race 3-inoculated F1 plants were only moderately resistant because they developed chlorosis presumably due to the Ptr ToxC-Tsc1 interaction. This work provides further understanding of genetic resistance in the wheat-tan spot system as well as important guidance for tan spot resistance breeding.
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Affiliation(s)
- Gayan K Kariyawasam
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Arron H Carter
- Department of Crop and Soil Science, Washington State University, Pullman, WA, 99164-6420, USA
| | - Jack B Rasmussen
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Justin Faris
- USDA-ARS Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, 58102, USA
| | - Steven S Xu
- USDA-ARS Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, 58102, USA
| | - Mohamed Mergoum
- Department of Plant Science, North Dakota State University, Fargo, ND, 58108, USA
- Department of Crop and Soil Sciences, University of Georgia, 1109 Experiment St, Griffin, GA, 30223, USA
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA.
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36
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Gao L, Jia J, Kong X. A SNP-Based Molecular Barcode for Characterization of Common Wheat. PLoS One 2016; 11:e0150947. [PMID: 26985664 PMCID: PMC4795793 DOI: 10.1371/journal.pone.0150947] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/22/2016] [Indexed: 11/19/2022] Open
Abstract
Wheat is grown as a staple crop worldwide. It is important to develop an effective genotyping tool for this cereal grain both to identify germplasm diversity and to protect the rights of breeders. Single-nucleotide polymorphism (SNP) genotyping provides a means for developing a practical, rapid, inexpensive and high-throughput assay. Here, we investigated SNPs as robust markers of genetic variation for typing wheat cultivars. We identified SNPs from an array of 9000 across a collection of 429 well-known wheat cultivars grown in China, of which 43 SNP markers with high minor allele frequency and variations discriminated the selected wheat varieties and their wild ancestors. This SNP-based barcode will allow for the rapid and precise identification of wheat germplasm resources and newly released varieties and will further assist in the wheat breeding program.
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Affiliation(s)
- LiFeng Gao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing, 100081, China
| | - JiZeng Jia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing, 100081, China
| | - XiuYing Kong
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing, 100081, China
- * E-mail:
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37
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Zhai H, Feng Z, Li J, Liu X, Xiao S, Ni Z, Sun Q. QTL Analysis of Spike Morphological Traits and Plant Height in Winter Wheat ( Triticum aestivum L.) Using a High-Density SNP and SSR-Based Linkage Map. FRONTIERS IN PLANT SCIENCE 2016; 7:1617. [PMID: 27872629 PMCID: PMC5097907 DOI: 10.3389/fpls.2016.01617] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 10/12/2016] [Indexed: 05/18/2023]
Abstract
Wheat yield can be enhanced by modifying the spike morphology and the plant height. In this study, a population of 191 F9 recombinant inbred lines (RILs) was developed from a cross between two winter cultivars Yumai 8679 and Jing 411. A dense genetic linkage map with 10,816 markers was constructed by incorporating single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker information. Five spike morphological traits and plant height were evaluated under nine environments for the RILs and parental lines, and the number of detected environmentally stable QTLs were 18 and three, respectively. The 1RS/1BL (rye) translocation increased both spike length and spikelet number with constant spikelet compactness. The QPht.cau-2D.1 was identical to gene Rht8, which decreased spike length without modifying spikelet number. Notably, four novel QTLs locating on chromosomes 1AS (QSc.cau-1A.1), 2DS (QSc.cau-2D.1), and 7BS (QSl.cau-7B.1 and QSl.cau-7B.2) were firstly identified in this study, which provide further insights into the genetic factors that shaped the spike morphology in wheat. Moreover, SNP markers tightly linked to previously reported QTLs will eventually facilitate future studies including their positional cloning or marker-assisted selection.
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Affiliation(s)
- Huijie Zhai
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Plant Gene Research CentreBeijing, China
| | - Zhiyu Feng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Plant Gene Research CentreBeijing, China
| | - Jiang Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Plant Gene Research CentreBeijing, China
| | - Xinye Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Plant Gene Research CentreBeijing, China
| | - Shihe Xiao
- Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Plant Gene Research CentreBeijing, China
- *Correspondence: Zhongfu Ni
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Plant Gene Research CentreBeijing, China
- Qixin Sun
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Maccaferri M, Ricci A, Salvi S, Milner SG, Noli E, Martelli PL, Casadio R, Akhunov E, Scalabrin S, Vendramin V, Ammar K, Blanco A, Desiderio F, Distelfeld A, Dubcovsky J, Fahima T, Faris J, Korol A, Massi A, Mastrangelo AM, Morgante M, Pozniak C, N'Diaye A, Xu S, Tuberosa R. A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:648-63. [PMID: 25424506 DOI: 10.1111/pbi.12288] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/26/2014] [Accepted: 10/03/2014] [Indexed: 05/20/2023]
Abstract
Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 data sets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum) and their ancestor (wild emmer, T. turgidum ssp. dicoccoides). The consensus map harboured 30 144 markers (including 26 626 SNPs and 791 SSRs) half of which were present in at least two component maps. The final map spanned 2631 cM of all 14 durum wheat chromosomes and, differently from the individual component maps, all markers fell within the 14 linkage groups. Marker density per genetic distance unit peaked at centromeric regions, likely due to a combination of low recombination rate in the centromeric regions and even gene distribution along the chromosomes. Comparisons with bread wheat indicated fewer regions with recombination suppression, making this consensus map valuable for mapping in the A and B genomes of both durum and bread wheat. Sequence similarity analysis allowed us to relate mapped gene-derived SNPs to chromosome-specific transcripts. Dense patterns of homeologous relationships have been established between the A- and B-genome maps and between nonsyntenic homeologous chromosome regions as well, the latter tracing to ancient translocation events. The gene-based homeologous relationships are valuable to infer the map location of homeologs of target loci/QTLs. Because most SNP and SSR markers were previously mapped in bread wheat, this consensus map will facilitate a more effective integration and exploitation of genes and QTL for wheat breeding purposes.
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Affiliation(s)
- Marco Maccaferri
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Andrea Ricci
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Sara Giulia Milner
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Enrico Noli
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | | | - Rita Casadio
- Biocomputing Group, University of Bologna, Bologna, Italy
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Simone Scalabrin
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Vera Vendramin
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | | | - Antonio Blanco
- Dipartimento di Biologia e Chimica Agro-forestale ed ambientale, Università di Bari, Aldo Moro, Bari, Italy
| | - Francesca Desiderio
- Consiglio per la ricerca e la sperimentazione in agricoltura, Genomics Research Centre, Fiorenzuola d'Arda, Italy
| | - Assaf Distelfeld
- Faculty of Life Sciences, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel
| | - Justin Faris
- USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA
| | - Abraham Korol
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel
| | - Andrea Massi
- Società Produttori Sementi Bologna (PSB), Argelato, Italy
| | - Anna Maria Mastrangelo
- Consiglio per la ricerca e la sperimentazione in agricoltura, Cereal Research Centre, Foggia, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Steven Xu
- USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA
| | - Roberto Tuberosa
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
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39
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Jordan KW, Wang S, Lun Y, Gardiner LJ, MacLachlan R, Hucl P, Wiebe K, Wong D, Forrest KL, Sharpe AG, Sidebottom CH, Hall N, Toomajian C, Close T, Dubcovsky J, Akhunova A, Talbert L, Bansal UK, Bariana HS, Hayden MJ, Pozniak C, Jeddeloh JA, Hall A, Akhunov E. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol 2015; 16:48. [PMID: 25886949 PMCID: PMC4389885 DOI: 10.1186/s13059-015-0606-4] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/04/2015] [Indexed: 12/21/2022] Open
Abstract
Background Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. Results A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. Conclusions Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0606-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherine W Jordan
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Shichen Wang
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Yanni Lun
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. .,Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA.
| | - Laura-Jayne Gardiner
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Ron MacLachlan
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Pierre Hucl
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Krysta Wiebe
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Debbie Wong
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | - Kerrie L Forrest
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | | | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0 W9, Canada.
| | | | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | | | - Timothy Close
- Department Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA.
| | - Jorge Dubcovsky
- Department Plant Sciences, University of California, Davis, CA, 95616, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - Alina Akhunova
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. .,Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA.
| | - Luther Talbert
- Department Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.
| | - Urmil K Bansal
- Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia.
| | - Harbans S Bariana
- Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia.
| | - Matthew J Hayden
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | - Curtis Pozniak
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | | | - Anthony Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Eduard Akhunov
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
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