1401
|
Qi PF, Jiang YF, Guo ZR, Chen Q, Ouellet T, Zong LJ, Wei ZZ, Wang Y, Zhang YZ, Xu BJ, Kong L, Deng M, Wang JR, Chen GY, Jiang QT, Lan XJ, Li W, Wei YM, Zheng YL. Transcriptional reference map of hormone responses in wheat spikes. BMC Genomics 2019; 20:390. [PMID: 31109305 PMCID: PMC6528200 DOI: 10.1186/s12864-019-5726-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/23/2019] [Indexed: 12/15/2022] Open
Abstract
Background Phytohormones are key regulators of plant growth, development, and signalling networks involved in responses to diverse biotic and abiotic stresses. Transcriptional reference maps of hormone responses have been reported for several model plant species such as Arabidopsis thaliana, Oryza sativa, and Brachypodium distachyon. However, because of species differences and the complexity of the wheat genome, these transcriptome data are not appropriate reference material for wheat studies. Results We comprehensively analysed the transcriptomic responses in wheat spikes to seven phytohormones, including indole acetic acid (IAA), gibberellic acid (GA), abscisic acid (ABA), ethylene (ET), cytokinin (CK), salicylic acid (SA), and methyl jasmonic acid (MeJA). A total of 3386 genes were differentially expressed at 24 h after the hormone treatments. Furthermore, 22.7% of these genes exhibited overlapping transcriptional responses for at least two hormones, implying there is crosstalk among phytohormones. We subsequently identified genes with expression levels that were significantly and differentially induced by a specific phytohormone (i.e., hormone-specific responses). The data for these hormone-responsive genes were then compared with the transcriptome data for wheat spikes exposed to biotic (Fusarium head blight) and abiotic (water deficit) stresses. Conclusion Our data were used to develop a transcriptional reference map of hormone responses in wheat spikes. Electronic supplementary material The online version of this article (10.1186/s12864-019-5726-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Peng-Fei Qi
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Chengdu, 611130, Sichuan, China. .,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Yun-Feng Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhen-Ru Guo
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qing Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Lu-Juan Zong
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhen-Zhen Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yan Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ya-Zhou Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Bin-Jie Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Li Kong
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ji-Rui Wang
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Chengdu, 611130, Sichuan, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Guo-Yue Chen
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Chengdu, 611130, Sichuan, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qian-Tao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiu-Jin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wei Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yu-Ming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| |
Collapse
|
1402
|
Gill HS, Li C, Sidhu JS, Liu W, Wilson D, Bai G, Gill BS, Sehgal SK. Fine Mapping of the Wheat Leaf Rust Resistance Gene Lr42. Int J Mol Sci 2019; 20:ijms20102445. [PMID: 31108903 PMCID: PMC6567072 DOI: 10.3390/ijms20102445] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/06/2019] [Accepted: 05/14/2019] [Indexed: 11/30/2022] Open
Abstract
Leaf rust caused by Puccinia triticina Eriks is one of the most problematic diseases of wheat throughout the world. The gene Lr42 confers effective resistance against leaf rust at both seedling and adult plant stages. Previous studies had reported Lr42 to be both recessive and dominant in hexaploid wheat; however, in diploid Aegilops tauschii (TA2450), we found Lr42 to be dominant by studying segregation in two independent F2 and their F2:3 populations. We further fine-mapped Lr42 in hexaploid wheat using a KS93U50/Morocco F5 recombinant inbred line (RIL) population to a 3.7 cM genetic interval flanked by markers TC387992 and WMC432. The 3.7 cM Lr42 region physically corresponds to a 3.16 Mb genomic region on chromosome 1DS based on the Chinese Spring reference genome (RefSeq v.1.1) and a 3.5 Mb genomic interval on chromosome 1 in the Ae. tauschii reference genome. This region includes nine nucleotide-binding domain leucine-rich repeat (NLR) genes in wheat and seven in Ae. tauschii, respectively, and these are the likely candidates for Lr42. Furthermore, we developed two kompetitive allele-specific polymorphism (KASP) markers (SNP113325 and TC387992) flanking Lr42 to facilitate marker-assisted selection for rust resistance in wheat breeding programs.
Collapse
Affiliation(s)
- Harsimardeep S Gill
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD 57006, USA.
| | - Chunxin Li
- National Engineering Laboratory of Wheat, Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China.
| | - Jagdeep S Sidhu
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD 57006, USA.
| | - Wenxuan Liu
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China.
| | - Duane Wilson
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetic Research Unit, Manhattan, KS 66506, USA.
| | - Bikram S Gill
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD 57006, USA.
| |
Collapse
|
1403
|
Genetic Dissection of Resistance to the Three Fungal Plant Pathogens Blumeria graminis, Zymoseptoria tritici, and Pyrenophora tritici-repentis Using a Multiparental Winter Wheat Population. G3-GENES GENOMES GENETICS 2019; 9:1745-1757. [PMID: 30902891 PMCID: PMC6505172 DOI: 10.1534/g3.119.400068] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Bread wheat (Triticum aestivum L.) is one of the world’s most important crop species. The development of new varieties resistant to multiple pathogens is an ongoing task in wheat breeding, especially in times of increasing demand for sustainable agricultural practices. Despite this, little is known about the relations between various fungal disease resistances at the genetic level, and the possible consequences for wheat breeding strategies. As a first step to fill this gap, we analyzed the genetic relations of resistance to the three fungal diseases – powdery mildew (PM), septoria tritici blotch (STB), and tan spot (TS) – using a winter wheat multiparent advanced generation intercross population. Six, seven, and nine QTL for resistance to PM, STB, and TS, respectively, were genetically mapped. Additionally, 15 QTL were identified for the three agro-morphological traits plant height, ear emergence time, and leaf angle distribution. Our results suggest that resistance to STB and TS on chromosome 2B is conferred by the same genetic region. Furthermore, we identified two genetic regions on chromosome 1AS and 7AL, which are associated with all three diseases, but not always in a synchronal manner. Based on our results, we conclude that parallel marker-assisted breeding for resistance to the fungal diseases PM, STB, and TS appears feasible. Knowledge of the genetic co-localization of alleles with contrasting effects for different diseases, such as on chromosome 7AL, allows the trade-offs of selection of these regions to be better understood, and ultimately determined at the genic level.
Collapse
|
1404
|
Devi U, Grewal S, Yang CY, Hubbart-Edwards S, Scholefield D, Ashling S, Burridge A, King IP, King J. Development and characterisation of interspecific hybrid lines with genome-wide introgressions from Triticum timopheevii in a hexaploid wheat background. BMC PLANT BIOLOGY 2019; 19:183. [PMID: 31060503 PMCID: PMC6501383 DOI: 10.1186/s12870-019-1785-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/17/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Triticum timopheevii (2n = 4x = 28; AtAtGG), is an important source for new genetic variation for wheat improvement with genes for potential disease resistance and salt tolerance. By generating a range of interspecific hybrid lines, T. timopheevii can contribute to wheat's narrow gene-pool and be practically utilised in wheat breeding programmes. Previous studies that have generated such introgression lines between wheat and its wild relatives have been unable to use high-throughput methods to detect the presence of wild relative segments in such lines. RESULTS A whole genome introgression approach, exploiting homoeologous recombination in the absence of the Ph1 locus, has resulted in the transfer of different chromosome segments from both the At and G genomes of T. timopheevii into wheat. These introgressions have been detected and characterised using single nucleotide polymorphism (SNP) markers present on a high-throughput Axiom® Genotyping Array. The analysis of these interspecific hybrid lines has resulted in the detection of 276 putative unique introgressions from T. timopheevii, thereby allowing the generation of a genetic map of T. timopheevii containing 1582 SNP markers, spread across 14 linkage groups representing each of the seven chromosomes of the At and G genomes of T. timopheevii. The genotyping of the hybrid lines was validated through fluorescence in situ hybridisation (FISH). Comparative analysis of the genetic map of T. timopheevii and the physical map of the hexaploid wheat genome showed that synteny between the two species is highly conserved at the macro-level and confirmed the presence of inter- and intra-genomic translocations within the At and G genomes of T. timopheevii that have been previously only detected through cytological techniques. CONCLUSIONS In this work, we report a set of SNP markers present on a high-throughput genotyping array, able to detect the presence of T. timopheevii in a hexaploid wheat background making it a potentially valuable tool for marker assisted selection (MAS) in wheat pre-breeding programs. These valuable resources of high-density molecular markers and wheat-T. timopheevii hybrid lines will greatly enhance the work being undertaken for wheat improvement through wild relative introgressions.
Collapse
Affiliation(s)
- Urmila Devi
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Surbhi Grewal
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Cai-Yun Yang
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Stella Hubbart-Edwards
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Duncan Scholefield
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Stephen Ashling
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Amanda Burridge
- Cereal Genomics Lab, Life Sciences Building, School of Biological Sciences, University of Bristol, Bristol, UK
| | - Ian P King
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Julie King
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK.
| |
Collapse
|
1405
|
Guo J, Zhang G, Song Y, Li Z, Ma S, Niu N, Wang J. Comparative proteomic analysis of multi-ovary wheat under heterogeneous cytoplasm suppression. BMC PLANT BIOLOGY 2019; 19:175. [PMID: 31046676 PMCID: PMC6498644 DOI: 10.1186/s12870-019-1778-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND DUOII is a multi-ovary wheat (Triticum aestivum L.) line with two or three pistils and three stamens in each floret. The multi-ovary trait of DUOII is controlled by a dominant gene, whose expression can be suppressed by the heterogeneous cytoplasm of TeZhiI (TZI), a line with the nucleus of common wheat and the cytoplasm of Aegilops. Crosses between female DUOII plants and male TZI plants resulted in multi-ovary F1s; whereas, the reciprocal crosses resulted in mono-ovary F1s. Although the multi-ovary trait is inherited as single trait controlled by a dominant allele in lines with a Triticum cytoplasm, the mechanism by which the special heterogeneous cytoplasm suppresses the expression of multi-ovary is not well understood. RESULTS Observing the developmental process, we found that the critical stage of additional pistil primordium development was when the young spikes were 2-6 mm long. Then, we compared the quantitative proteomic profiles of 2-6 mm long young spikes obtained from the reciprocal crosses between DUOII and TZI. A total of 90 differentially expressed proteins were identified and analyzed based on their biological functions. These proteins had obvious functional pathways mainly implicated in chloroplast metabolism, nuclear and cell division, plant respiration, protein metabolism, and flower development. Importantly, we identified two key proteins, Flowering Locus K Homology Domain and PEPPER, which are known to play an essential role in the specification of pistil organ identity. By drawing relationships between the 90 differentially expressed proteins, we found that these proteins revealed a complex network which is associated with multi-ovary gene expression under heterogeneous cytoplasmic suppression. CONCLUSIONS Our proteomic analysis has identified certain differentially expressed proteins in 2-6 mm long young spikes, which was the critical stage of additional primordium development. This paper provided a universal proteomic profiling involved in the cytoplasmic suppression of wheat floral meristems; and our findings have laid a solid foundation for further mechanistic studies on the underlying mechanisms that control the heterogeneous cytoplasm-induced suppression of the nuclear multi-ovary gene in wheat.
Collapse
Affiliation(s)
- Jialin Guo
- College of Agronomy, National Yangling Agriculture Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Gaisheng Zhang
- College of Agronomy, National Yangling Agriculture Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Yulong Song
- College of Agronomy, National Yangling Agriculture Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Zheng Li
- College of Agronomy, National Yangling Agriculture Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Shoucai Ma
- College of Agronomy, National Yangling Agriculture Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Na Niu
- College of Agronomy, National Yangling Agriculture Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Junwei Wang
- College of Agronomy, National Yangling Agriculture Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A & F University, Yangling, 712100 Shaanxi China
| |
Collapse
|
1406
|
Mirzaghaderi G, Mason AS. Broadening the bread wheat D genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1295-1307. [PMID: 30739154 DOI: 10.1007/s00122-019-03299-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 02/02/2019] [Indexed: 05/21/2023]
Abstract
Although Ae. tauschii has been extensively utilised for wheat breeding, the D-genome-containing allopolyploids have largely remained unexploited. In this review, we discuss approaches that can be used to exploit the D genomes of the different Aegilops species for the improvement of bread wheat. The D genome of allohexaploid bread wheat (Triticum aestivum, 2n = AABBDD) is the least diverse of the three wheat genomes and is unarguably less diverse than that of diploid progenitor Aegilops tauschii (2n = DD). Useful genetic variation and phenotypic traits also exist within each of the wheat group species containing a copy of the D genome: allopolyploid Aegilops species Ae. cylindrica (2n = DcDcCcCc), Ae. crassa 4x (2n = D1D1XcrXcr), Ae. crassa 6x (2n = D1D1XcrXcrDcrDcr), Ae. ventricosa (2n = DvDvNvNv), Ae. vavilovii (2n = D1D1XcrXcrSvSv) and Ae. juvenalis (2n = D1D1XcrXcrUjUj). Although Ae. tauschii has been extensively utilised for wheat breeding, the D-genome-containing allopolyploids have largely remained unexploited. Some of these D genomes appear to be modified relative to the bread wheat and Ae. tauschii D genomes, and others present in the allopolyploids may also contain useful variation as a result of adaptation to an allopolyploid, multi-genome environment. We summarise the genetic relationships, karyotypic variation and phenotypic traits known to be present in each of the D genome species that could be of relevance for bread wheat improvement and discuss approaches that can be used to exploit the D genomes of the different Aegilops species for the improvement of bread wheat. Better understanding of factors controlling chromosome inheritance and recombination in wheat group interspecific hybrids, as well as effective utilisation of new and developing genetics and genomics technologies, have great potential to improve the agronomic potential of the bread wheat D genome.
Collapse
Affiliation(s)
- Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran.
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| |
Collapse
|
1407
|
Cseh A, Yang C, Hubbart-Edwards S, Scholefield D, Ashling SS, Burridge AJ, Wilkinson PA, King IP, King J, Grewal S. Development and validation of an exome-based SNP marker set for identification of the St, J r and J vs genomes of Thinopyrym intermedium in a wheat background. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1555-1570. [PMID: 30767030 PMCID: PMC6476854 DOI: 10.1007/s00122-019-03300-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/02/2019] [Indexed: 05/19/2023]
Abstract
KEY MESSAGE Cytogenetic analysis and array-based SNP genotyping of wheat- Th. intermedium introgression lines allowed identification of 634 chromosome-specific SNP markers across all twenty-one chromosomes of Th. intermedium (StJ r J vs , 2 n = 6 x = 42). Thinopyrum intermedium (2n = 6x = 42, StJrJvs) is one of the most promising reservoirs of useful genes including tolerance to abiotic stresses, perenniality and disease resistance not available in the cultivated bread wheat. The transfer of genetic diversity from wild species to wheat offers valuable responses to the effects of climate change. The new array-based single-nucleotide polymorphism (SNP) marker technology provides cheap and easy-to-use molecular markers for marker-assisted selection (MAS) in wheat breeding programmes. Here, we focus on the generation of a new chromosome-specific SNP marker set that can be used to characterize and identify the Th. intermedium chromosomes or chromosome segments transferred into wheat. A progressive investigation of marker development was conducted using 187 various newly developed wheat-Th. intermedium introgression lines and the Axiom® Wheat-Relative Genotyping array. We employed molecular cytogenetic techniques to clarify the genome constitution of the Th. intermedium parental lines and validated 634 chromosome-specific SNPs. Our data confirmed the allohexaploid nature of Th. intermedium and demonstrated that the St genome-specific GISH signal and markers are present at the centromeric regions of chromosomes 1Jvs, 2Jvs, 3Jvs and 7Jvs. The SNP markers presented here will be introduced into current wheat improvement programmes, offering a significant speed-up in wheat breeding and making it possible to deal with the transfer of the full genetic potential of Th. intermedium into wheat.
Collapse
Affiliation(s)
- Andras Cseh
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- Molecular Breeding Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Caiyun Yang
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Stella Hubbart-Edwards
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Stephen S Ashling
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | | | | | - Ian P King
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK.
| |
Collapse
|
1408
|
Ma J, Qin N, Cai B, Chen G, Ding P, Zhang H, Yang C, Huang L, Mu Y, Tang H, Liu Y, Wang J, Qi P, Jiang Q, Zheng Y, Liu C, Lan X, Wei Y. Identification and validation of a novel major QTL for all-stage stripe rust resistance on 1BL in the winter wheat line 20828. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1363-1373. [PMID: 30680420 DOI: 10.1007/s00122-019-03283-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 01/10/2019] [Indexed: 05/24/2023]
Abstract
A major, likely novel stripe rust resistance QTL for all-stage resistance on chromosome arm 1BL identified in a 1.76-cM interval using a saturated linkage map was validated in four populations with different genetic backgrounds. Stripe rust is a globally important disease of wheat. Identification and utilization of new resistance genes are essential for breeding resistant cultivars. Wheat line 20828 has exhibited high levels of stripe rust resistance for over a decade. However, the genetics of stripe rust resistance in this line has not been studied. A set of 199 recombinant inbred lines (RILs) were developed from a cross between 20828 and a susceptible cultivar Chuannong 16. The RIL population was genotyped with the Wheat55K SNP (single nucleotide polymorphism) array and SSR (simple sequence repeat) markers and evaluated in four environments with current predominant Puccinia striiformis f. sp. tritici t races including CYR32, CYR33 and CYR34. Four stable QTL were located on chromosomes 1B (2 QTL), 4A and 6A. Among them, the major QTL, QYr.sicau-1B.1 (LOD = 23-28, PVE = 16-39%), was localized to a 1.76-cM interval flanked by SSR markers Xwmc216 and Xwmc156 on chromosome 1BL. Eight resistance genes were previously identified in the physical interval of QYr.sicau-1B.1. Compared with previous studies, QYr.sicau-1B.1 is a new gene for resistant to stripe rust. It was further verified by analysis of the closely linked SSR markers Xwmc216 and Xwmc156 in four other populations with different genetic backgrounds. QYr.sicau-1B.1 reduced the stripe rust disease index by up to 82.8%. Three minor stable QTL (located on chromosomes 1B, 4A and 6A, respectively) also added to the resistance level of QYr.sicau-1B.1. Our results provide valuable information for further fine mapping and cloning as well as molecular-assisted breeding with QYr.sicau-1B.1.
Collapse
Affiliation(s)
- Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Nana Qin
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ben Cai
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Puyang Ding
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Han Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Congcong Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lin Huang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yang Mu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Huaping Tang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Pengfei Qi
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Chunji Liu
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, St Lucia, QLD, 4067, Australia
| | - Xiujin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| |
Collapse
|
1409
|
Ustyantsev KV, Goncharov NP. Homology of Genes Controlling Architectonics of Vegetative and Generative Organs in Barley and Rice and Their Application for Wheat Biodiversity Expansion and Breeding. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419050156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
1410
|
Wu P, Hu J, Zou J, Qiu D, Qu Y, Li Y, Li T, Zhang H, Yang L, Liu H, Zhou Y, Zhang Z, Li J, Liu Z, Li H. Fine mapping of the wheat powdery mildew resistance gene Pm52 using comparative genomics analysis and the Chinese Spring reference genomic sequence. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1451-1461. [PMID: 30719526 DOI: 10.1007/s00122-019-03291-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/19/2019] [Indexed: 05/07/2023]
Abstract
A high-resolution genetic linkage map was constructed using the comparative genomics analysis approach and the wheat reference genome, which placed wheat powdery mildew resistance gene Pm52 in a 0.21-cM genetic interval on chromosome arm 2BL. The gene Pm52 confers resistance to powdery mildew and has been previously mapped on chromosome arm 2BL in winter wheat cultivar Liangxing 99. Because of its effectiveness against the disease, this study was initiated to finely map Pm52 using the comparative genomics analysis approach and the wheat reference genomic sequence. Based on the EST sequences that were located in the chromosome region flanking Pm52, four EST-SSR markers were developed, and another nine SSR markers were developed using the comparative genomics technology. These thirteen markers were integrated into a genetic linkage map using an F2:3 subpopulation of the Liangxing 99 × Zhongzuo 9504 cross. Pm52 was mapped within a 3.2-cM genetic interval in the subpopulation that corresponded to a ~40-Mb genomic interval on chromosome arm 2BL of the Chinese Spring reference genome. The Pm52-flanking markers Xicsl163 and Xicsl62 identified 344 recombinant individuals from 8820 F2 plants. Nine SSR markers generated from the Chinese Spring genomic interval were incorporated into a high-resolution genetic linkage map, which placed Pm52 in a 0.21-cM genetic interval corresponding to 5.6-Mb genomic region. The constructed high-resolution genetic linkage map will facilitate the map-based cloning of Pm52 and its marker-assisted selection.
Collapse
Affiliation(s)
- Peipei Wu
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Jinghuang Hu
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jingwei Zou
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dan Qiu
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunfeng Qu
- College of Life Science and Technology, Harbin Normal University, Harbin, 150080, China
| | - Yahui Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Teng Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongjun Zhang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Yang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongwei Liu
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Zhou
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhongjun Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Jingting Li
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, 467000, China.
| | - Zhiyong Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Hongjie Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
1411
|
Zeng Q, Wu J, Liu S, Huang S, Wang Q, Mu J, Yu S, Han D, Kang Z. A major QTL co-localized on chromosome 6BL and its epistatic interaction for enhanced wheat stripe rust resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1409-1424. [PMID: 30707240 DOI: 10.1007/s00122-019-03288-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 01/16/2019] [Indexed: 05/27/2023]
Abstract
Co-localization of a major QTL for wheat stripe rust resistance to a 3.9-cM interval on chromosome 6BL across both populations and another QTL on chromosome 2B with epistatic interaction. Cultivars with diverse resistance are the optimal strategy to minimize yield losses caused by wheat stripe rust (Puccinia striiformis f. sp. tritici). Two wheat populations involving resistant wheat lines P10078 and Snb"S" from CIMMYT were evaluated for stripe rust response in multiple environments. Pool analysis by Wheat660K SNP array showed that the overlapping interval on chromosome 6B likely harbored a major QTL between two populations. Then, linkage maps were constructed using KASP markers, and a co-localized locus with large effect on chromosome 6BL was detected using QTL analysis in both populations. The coincident QTL, named QYr.nwafu-6BL.2, explained 59.7% of the phenotypic maximum variation in the Mingxian 169 × P10078 and 52.5% in the Zhengmai 9023 × Snb"S" populations, respectively. This co-localization interval spanning 3.9 cM corresponds to ~ 30.5-Mb genomic region of the newest common wheat reference genome (IWGSC RefSeq v.1.0). In addition, another QTL was also detected on chromosome 2B in Zhengmai 9023 × Snb"S" population and it can accelerate expression of QYr.nwafu-6BL.2 to enhance resistance with epistatic interaction. Allowing for Pst response, marker genotypes, pedigree analysis and relative genetic distance, QYr.nwafu-6BL.2 is likely to be a distinct adult plant resistance QTL. Haplotype analysis of QYr.nwafu-6BL.2 revealed specific SNPs or alleles in the target region from a diversity panel of 176 unrelated wheat accessions. This QTL region provides opportunity for further map-based cloning, and haplotypes analysis enables pyramiding favorable alleles into commercial cultivars by marker-assisted selection.
Collapse
Affiliation(s)
- Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jingmei Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shizhou Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
| |
Collapse
|
1412
|
Narang D, Kaur S, Steuernagel B, Ghosh S, Dhillon R, Bansal M, Uauy C, Wulff BBH, Chhuneja P. Fine mapping of Aegilops peregrina co-segregating leaf and stripe rust resistance genes to distal-most end of 5DS. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1473-1485. [PMID: 30706082 DOI: 10.1007/s00122-019-03293-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
Novel rust resistance genes LrP and YrP from Ae. peregrina identified on chromosome 5D and the linked markers will aid deployment of these genes in combination with other major/minor genes. Aegilops peregrina, a wild tetraploid relative of wheat with genome constitution UUSS, displays genetic variation for resistance to leaf and stripe (yellow) rust. The wheat Ae. peregrina introgression line, IL pau16058, harbouring leaf and stripe rust resistance, was crossed with wheat cv. WL711 to generate an F2:3 mapping population. Inheritance studies on this population indicated the transfer of dominant co-segregating resistance to leaf and stripe rust. Ethyl methane sulphonate mutagenesis of IL pau16058 identified independent loss-of-function mutants for leaf and stripe rust resistance, indicating that the leaf and stripe rust resistance is controlled by independent genes, herein designated LrP and YrP, respectively. A high-resolution genetic map of LrP and YrP was constructed using the Illumina Infinium iSelect 90K wheat array and resistance gene enrichment sequencing (RenSeq) markers. The map spans 4.19 cM on the distal-most region of the short arm of chromosome 5D, consisting of eight SNP markers and one microsatellite marker. LrP and YrP co-segregated with markers BS00163889 and 5DS44573_snp and was flanked distally by the SNP marker BS00129707 and proximally by 5DS149010, defining a 15.71 Mb region in the RefSeq v1.0 genome assembly.
Collapse
Affiliation(s)
- Deepika Narang
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | | | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Roopan Dhillon
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Mitaly Bansal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| |
Collapse
|
1413
|
Balfourier F, Bouchet S, Robert S, De Oliveira R, Rimbert H, Kitt J, Choulet F, Paux E. Worldwide phylogeography and history of wheat genetic diversity. SCIENCE ADVANCES 2019; 5:eaav0536. [PMID: 31149630 PMCID: PMC6541461 DOI: 10.1126/sciadv.aav0536] [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: 08/09/2018] [Accepted: 04/22/2019] [Indexed: 05/05/2023]
Abstract
Since its domestication in the Fertile Crescent ~8000 to 10,000 years ago, wheat has undergone a complex history of spread, adaptation, and selection. To get better insights into the wheat phylogeography and genetic diversity, we describe allele distribution through time using a set of 4506 landraces and cultivars originating from 105 different countries genotyped with a high-density single-nucleotide polymorphism array. Although the genetic structure of landraces is collinear to ancient human migration roads, we observe a reshuffling through time, related to breeding programs, with the appearance of new alleles enriched with structural variations that may be the signature of introgressions from wild relatives after 1960.
Collapse
Affiliation(s)
- François Balfourier
- GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
- Corresponding author. (F.B.); (E.P.)
| | - Sophie Bouchet
- GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Sandra Robert
- GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Romain De Oliveira
- GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Hélène Rimbert
- GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Jonathan Kitt
- GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Frédéric Choulet
- GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | | | | | - Etienne Paux
- GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
- Corresponding author. (F.B.); (E.P.)
| |
Collapse
|
1414
|
He F, Pasam R, Shi F, Kant S, Keeble-Gagnere G, Kay P, Forrest K, Fritz A, Hucl P, Wiebe K, Knox R, Cuthbert R, Pozniak C, Akhunova A, Morrell PL, Davies JP, Webb SR, Spangenberg G, Hayes B, Daetwyler H, Tibbits J, Hayden M, Akhunov E. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nat Genet 2019; 51:896-904. [PMID: 31043759 DOI: 10.1038/s41588-019-0382-2] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 02/26/2019] [Indexed: 11/09/2022]
Abstract
Introgression is a potential source of beneficial genetic diversity. The contribution of introgression to adaptive evolution and improvement of wheat as it was disseminated worldwide remains unknown. We used targeted re-sequencing of 890 diverse accessions of hexaploid and tetraploid wheat to identify wild-relative introgression. Introgression, and selection for improvement and environmental adaptation, each reduced deleterious allele burden. Introgression increased diversity genome wide and in regions harboring major agronomic genes, and contributed alleles explaining a substantial proportion of phenotypic variation. These results suggest that historic gene flow from wild relatives made a substantial contribution to the adaptive diversity of modern bread wheat.
Collapse
Affiliation(s)
- Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Raj Pasam
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Fan Shi
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Surya Kant
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | | | - Pippa Kay
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Kerrie Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Allan Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Pierre Hucl
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Krystalee Wiebe
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ron Knox
- Swift Current Research and Development Centre, Swift Current, Saskatchewan, Canada
| | - Richard Cuthbert
- Swift Current Research and Development Centre, Swift Current, Saskatchewan, Canada
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, USA
| | - John P Davies
- Corteva Agriscience, Agriculture Division of DowDuPont, Indianapolis, IN, USA
| | - Steve R Webb
- Corteva Agriscience, Agriculture Division of DowDuPont, Indianapolis, IN, USA
| | - German Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Ben Hayes
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, University of Queensland, St Lucia, Queensland, Australia
| | - Hans Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Josquin Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia.
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
| |
Collapse
|
1415
|
Insights on the Proteases Involved in Barley and Wheat Grain Germination. Int J Mol Sci 2019; 20:ijms20092087. [PMID: 31035313 PMCID: PMC6539298 DOI: 10.3390/ijms20092087] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/22/2019] [Accepted: 04/24/2019] [Indexed: 01/11/2023] Open
Abstract
Seed storage proteins must be hydrolyzed by proteases to deliver the amino acids essential for embryo growth and development. Several groups of proteases involved in this process have been identified in both the monocot and the dicot species. This review focuses on the implication of proteases during germination in two cereal species, barley and wheat, where proteolytic control during the germination process has considerable economic importance. Formerly, the participation of proteases during grain germination was inferred from reports of proteolytic activities, the expression of individual genes, or the presence of individual proteins and showed a prominent role for papain-like and legumain-like cysteine proteases and for serine carboxypeptidases. Nowadays, the development of new technologies and the release of the genomic sequences of wheat and barley have permitted the application of genome-scale approaches, such as those used in functional genomics and proteomics. Using these approaches, the repertoire of proteases known to be involved in germination has increased and includes members of distinct protease families. The development of novel techniques based on shotgun proteomics, activity-based protein profiling, and comparative and structural genomics will help to achieve a general view of the proteolytic process during germination.
Collapse
|
1416
|
Sheoran S, Jaiswal S, Kumar D, Raghav N, Sharma R, Pawar S, Paul S, Iquebal MA, Jaiswar A, Sharma P, Singh R, Singh CP, Gupta A, Kumar N, Angadi UB, Rai A, Singh GP, Kumar D, Tiwari R. Uncovering Genomic Regions Associated With 36 Agro-Morphological Traits in Indian Spring Wheat Using GWAS. FRONTIERS IN PLANT SCIENCE 2019; 10:527. [PMID: 31134105 PMCID: PMC6511880 DOI: 10.3389/fpls.2019.00527] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/04/2019] [Indexed: 05/13/2023]
Abstract
Wheat genetic improvement by integration of advanced genomic technologies is one way of improving productivity. To facilitate the breeding of economically important traits in wheat, SNP loci and underlying candidate genes associated with the 36 agro-morphological traits were studied in a diverse panel of 404 genotypes. By using Breeders' 35K Axiom array in a comprehensive genome-wide association study covering 4364.79 cM of the wheat genome and applying a compressed mixed linear model, a total of 146 SNPs (-log10 P ≥ 4) were found associated with 23 traits out of 36 traits studied explaining 3.7-47.0% of phenotypic variance. To reveal this a subset of 260 genotypes was characterized phenotypically for six quantitative traits [days to heading (DTH), days to maturity (DTM), plant height (PH), spike length (SL), awn length (Awn_L), and leaf length (Leaf_L)] under five environments. Gene annotations mined ∼38 putative candidate genes which were confirmed using tissue and stage specific gene expression data from RNA Seq. We observed strong co-localized loci for four traits (glume pubescence, SL, PH, and awn color) on chromosome 1B (24.64 cM) annotated five putative candidate genes. This study led to the discovery of hitherto unreported loci for some less explored traits (such as leaf sheath wax, awn attitude, and glume pubescence) besides the refined chromosomal regions of known loci associated with the traits. This study provides valuable information of the genetic loci and their potential genes underlying the traits such as awn characters which are being considered as important contributors toward yield enhancement.
Collapse
Affiliation(s)
- Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sarika Jaiswal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Deepender Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Nishu Raghav
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Ruchika Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sushma Pawar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Surinder Paul
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - M. A. Iquebal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Akanksha Jaiswar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Rajender Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Arun Gupta
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Neeraj Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - U. B. Angadi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - G. P. Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Dinesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| |
Collapse
|
1417
|
Ye X, Li J, Cheng Y, Yao F, Long L, Yu C, Wang Y, Wu Y, Li J, Wang J, Jiang Q, Li W, Ma J, Wei Y, Zheng Y, Chen G. Genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in Sichuan wheat. BMC PLANT BIOLOGY 2019; 19:147. [PMID: 30991940 PMCID: PMC6469213 DOI: 10.1186/s12870-019-1764-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 04/08/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Stripe rust (also called yellow rust) is a common and serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici. The narrow genetic basis of modern wheat cultivars and rapid evolution of the rust pathogen have been responsible for periodic and devastating epidemics of wheat rust diseases. In this study, we conducted a genome-wide association study with 44,059 single nucleotide polymorphism markers to identify loci associated with resistance to stripe rust in 244 Sichuan wheat accessions, including 79 landraces and 165 cultivars, in six environments. RESULTS In all the field assessments, 24 accessions displayed stable high resistance to stripe rust. Significant correlations among environments were observed for both infection (IT) and disease severity (DS), and high heritability levels were found for both IT and DS. Using mixed linear models, 12 quantitative trait loci (QTLs) significantly associated with IT and/or DS were identified. Two QTLs were mapped on chromosomes 5AS and 5AL and were distant from previously identified stripe rust resistance genes or QTL regions, indicating that they may be novel resistance loci. CONCLUSIONS Our results revealed that resistance alleles to stripe rust were accumulated in Sichuan wheat germplasm, implying direct or indirect selection for improved stripe rust resistance in elite wheat breeding programs. The identified stable QTLs or favorable alleles could be important chromosome regions in Sichuan wheat that controlled the resistance to stripe rust. These markers can be used molecular marker-assisted breeding of Sichuan wheat cultivars, and will be useful in the ongoing effort to develop new wheat cultivars with strong resistance to stripe rust.
Collapse
Affiliation(s)
- Xueling Ye
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jian Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yukun Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Can Yu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yu Wu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jing Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China.
| |
Collapse
|
1418
|
Gardiner LJ, Wingen LU, Bailey P, Joynson R, Brabbs T, Wright J, Higgins JD, Hall N, Griffiths S, Clavijo BJ, Hall A. Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency. Genome Biol 2019; 20:69. [PMID: 30982471 PMCID: PMC6463664 DOI: 10.1186/s13059-019-1675-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 03/13/2019] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. A lack of recombination limits breeding efforts in crops; therefore, increasing recombination rates can reduce linkage drag and generate new genetic combinations. RESULTS We use computational analysis of 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat (Triticum aestivum). We observe that high-frequency crossover sites are shared between populations and that closely related parents lead to populations with more similar crossover patterns. We demonstrate that gene conversion is more prevalent and covers more of the genome in wheat than in other plants, making it a critical process in the generation of new haplotypes, particularly in centromeric regions where crossovers are rare. We identify quantitative trait loci for altered gene conversion and crossover frequency and confirm functionality for a novel RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages including Arabidopsis. CONCLUSIONS This is the first gene to be demonstrated to be involved in gene conversion in wheat. Harnessing the RecQ helicase has the potential to break linkage drag utilizing widespread gene conversions.
Collapse
Affiliation(s)
| | | | | | | | | | | | - James D. Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH UK
| | - Neil Hall
- Earlham Institute, Norwich, NR4 7UZ UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | | | | | - Anthony Hall
- Earlham Institute, Norwich, NR4 7UZ UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| |
Collapse
|
1419
|
Xiao J, Hu R, Gu T, Han J, Qiu D, Su P, Feng J, Chang J, Yang G, He G. Genome-wide identification and expression profiling of trihelix gene family under abiotic stresses in wheat. BMC Genomics 2019; 20:287. [PMID: 30975075 PMCID: PMC6460849 DOI: 10.1186/s12864-019-5632-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/21/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The trihelix gene family is a plant-specific transcription factor family that plays important roles in plant growth, development, and responses to abiotic stresses. However, to date, no systemic characterization of the trihelix genes has yet been conducted in wheat and its close relatives. RESULTS We identified a total of 94 trihelix genes in wheat, as well as 22 trihelix genes in Triticum urartu, 29 in Aegilops tauschii, and 31 in Brachypodium distachyon. We analyzed the chromosomal locations and orthology relations of the identified trihelix genes, and no trihelix gene was found to be located on chromosome 7A, 7B, or 7D of wheat, thereby reflecting the uneven distributions of wheat trihelix genes. Phylogenetic analysis indicated that the 186 identified trihelix proteins in wheat, rice, B. distachyon, and Arabidopsis were clustered into five major clades. The trihelix genes belonging to the same clades usually shared similar motif compositions and exon/intron structural patterns. Five pairs of tandem duplication genes and three pairs of segmental duplication genes were identified in the wheat trihelix gene family, thereby validating the supposition that more intrachromosomal gene duplication events occur in the genome of wheat than in that of other grass species. The tissue-specific expression and differential expression profiling of the identified genes under cold and drought stresses were analyzed by using RNA-seq data. qRT-PCR was also used to confirm the expression profiles of ten selected wheat trihelix genes under multiple abiotic stresses, and we found that these genes mainly responded to salt and cold stresses. CONCLUSIONS In this study, we identified trihelix genes in wheat and its close relatives and found that gene duplication events are the main driving force for trihelix gene evolution in wheat. Our expression profiling analysis demonstrated that wheat trihelix genes responded to multiple abiotic stresses, especially salt and cold stresses. The results of our study built a basis for further investigation of the functions of wheat trihelix genes and provided candidate genes for stress-resistant wheat breeding programs.
Collapse
Affiliation(s)
- Jie Xiao
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Rui Hu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Ting Gu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Jiapeng Han
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Ding Qiu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Peipei Su
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Jialu Feng
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| |
Collapse
|
1420
|
Alahmad S, El Hassouni K, Bassi FM, Dinglasan E, Youssef C, Quarry G, Aksoy A, Mazzucotelli E, Juhász A, Able JA, Christopher J, Voss-Fels KP, Hickey LT. A Major Root Architecture QTL Responding to Water Limitation in Durum Wheat. FRONTIERS IN PLANT SCIENCE 2019; 10:436. [PMID: 31024600 PMCID: PMC6468307 DOI: 10.3389/fpls.2019.00436] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/22/2019] [Indexed: 05/21/2023]
Abstract
The optimal root system architecture (RSA) of a crop is context dependent and critical for efficient resource capture in the soil. Narrow root growth angle promoting deeper root growth is often associated with improved access to water and nutrients in deep soils during terminal drought. RSA, therefore is a drought-adaptive trait that could minimize yield losses in regions with limited rainfall. Here, GWAS for seminal root angle (SRA) identified seven marker-trait associations clustered on chromosome 6A, representing a major quantitative trait locus (qSRA-6A) which also displayed high levels of pairwise LD (r 2 = 0.67). Subsequent haplotype analysis revealed significant differences between major groups. Candidate gene analysis revealed loci related to gravitropism, polar growth and hormonal signaling. No differences were observed for root biomass between lines carrying hap1 and hap2 for qSRA-6A, highlighting the opportunity to perform marker-assisted selection for the qSRA-6A locus and directly select for wide or narrow RSA, without influencing root biomass. Our study revealed that the genetic predisposition for deep rooting was best expressed under water-limitation, yet the root system displayed plasticity producing root growth in response to water availability in upper soil layers. We discuss the potential to deploy root architectural traits in cultivars to enhance yield stability in environments that experience limited rainfall.
Collapse
Affiliation(s)
- Samir Alahmad
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Khaoula El Hassouni
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
- International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Eric Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Chvan Youssef
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Georgia Quarry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Alpaslan Aksoy
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | | | - Angéla Juhász
- School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Jason A. Able
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Urrbrae, SA, Australia
| | - Jack Christopher
- Leslie Research Facility, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Kai P. Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Lee T. Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
1421
|
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.
Collapse
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
| |
Collapse
|
1422
|
Durum wheat genome highlights past domestication signatures and future improvement targets. Nat Genet 2019; 51:885-895. [PMID: 30962619 DOI: 10.1038/s41588-019-0381-3] [Citation(s) in RCA: 369] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/22/2019] [Indexed: 12/13/2022]
Abstract
The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and breeding. Regions exhibiting strong signatures of genetic divergence associated with domestication and breeding were widespread in the genome with several major diversity losses in the pericentromeric regions. A locus on chromosome 5B carries a gene encoding a metal transporter (TdHMA3-B1) with a non-functional variant causing high accumulation of cadmium in grain. The high-cadmium allele, widespread among durum cultivars but undetected in wild emmer accessions, increased in frequency from domesticated emmer to modern durum wheat. The rapid cloning of TdHMA3-B1 rescues a wild beneficial allele and demonstrates the practical use of the Svevo genome for wheat improvement.
Collapse
|
1423
|
Wheat landraces with low mycorrhizing ability at field respond differently to inoculation with artificial or indigenous arbuscular mycorrhizal fungal communities. Symbiosis 2019. [DOI: 10.1007/s13199-019-00612-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
1424
|
Senapati N, Semenov MA. Assessing yield gap in high productive countries by designing wheat ideotypes. Sci Rep 2019; 9:5516. [PMID: 30940895 PMCID: PMC6445095 DOI: 10.1038/s41598-019-40981-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/27/2019] [Indexed: 01/17/2023] Open
Abstract
Designing crop ideotypes in silico is a powerful tool to explore the crop yield potential and yield gap. We defined yield gap as the difference between yield potential of a crop ideotype optimized under local environment and yield of an existing cultivar under optimal management. Wheat ideotypes were designed for the current climate using the Sirius model for both water-limited and irrigated conditions in two high wheat-productive countries viz. the United Kingdom (UK) and New Zealand (NZ) with the objective of estimating yield gap. The mean ideotype yields of 15.0-19.0 t ha-1 were achieved in water-limited conditions in the UK and NZ, whereas 15.6-19.5 t ha-1 under irrigated conditions. Substantial yield gaps were found in both water-limited, 28-31% (4-6 t ha-1), and irrigated conditions, 30-32% (5-6 t ha-1) in the UK and NZ. Both yield potential (25-27%) and yield gap (32-38%) were greater in NZ than the UK. Ideotype design is generic and could apply globally for estimating yield gap. Despite wheat breeding efforts, the considerable yield gap still potentially exists in high productive countries such as the UK and NZ. To accelerate breeding, wheat ideotypes can provide the key traits for wheat improvement and closing the yield gap.
Collapse
Affiliation(s)
- Nimai Senapati
- Department of Plant Sciences, Rothamsted Research, West Common, Harpenden, Herts, AL5 2JQ, United Kingdom.
| | - Mikhail A Semenov
- Department of Plant Sciences, Rothamsted Research, West Common, Harpenden, Herts, AL5 2JQ, United Kingdom
| |
Collapse
|
1425
|
CRISPR-based genome editing in wheat: a comprehensive review and future prospects. Mol Biol Rep 2019; 46:3557-3569. [PMID: 30941642 DOI: 10.1007/s11033-019-04761-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/14/2019] [Indexed: 01/26/2023]
Abstract
CRISPR technology has vividly increased its applications in last five years for genome editing in a wide range of organisms from bacteria to plants. It is mostly applied in the field of mammalian research. This emerging versatile tool can be utilized in crop improvement by targeting various traits to increase economic value and adaptability of the crop species under changing climate. In plants, Arabidopsis and rice are the most studied plant species in genome editing through CRISPR technology. Wheat is lagging behind in the utilization of CRISPR based genome modifications. The hexaploid, large genome size and the recalcitrant nature in terms of tissue culture are the major obstacles for CRISPR utilization in wheat. Recently, the IWGSC released the high quality of reference genome for wheat which will greatly accelerate the application of CRISPR-based genome engineering in wheat and helps to resolve the global issue of food security in coming decades. The exogenous DNA-free improved mutants with CRISPR technology having desired traits will increase the productivity under biotic and abiotic stress conditions. To address complex traits involving multigene, recently developed multiplex genome editing toolkits can be used. This is a first review of its kind in which the practical utilization and updates on CRISPR validation in wheat along with its future prospects for use of this technology in wheat improvement are comprehensively discussed. Thus, the compiled information will immensely benefit the researchers for utilization of CRISPR system in wheat improvement across the globe.
Collapse
|
1426
|
Gardiner LJ, Brabbs T, Akhunov A, Jordan K, Budak H, Richmond T, Singh S, Catchpole L, Akhunov E, Hall A. Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat. Gigascience 2019. [PMID: 30715311 DOI: 10.1101/363663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Whole-genome shotgun resequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome, making it difficult to unambiguously assign variation. Resequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented complementary DNA/exon or gene-based probe sets in which the promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. RESULTS We present and validate 2 gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high-confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low-confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for single-nucleotide polymorphism calling while significantly reducing cost per sample for gene and putative promoter capture. CONCLUSIONS We show that a capture design employing an "island strategy" can enable analysis of the large gene/putative promoter space of wheat with only 2 × 160 Mbp probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.
Collapse
Affiliation(s)
- Laura-Jayne Gardiner
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
- IBM Research, The Hartree Centre STFC Laboratory, Sci-Tech Daresbury, Warrington, WA4 4AD, UK
| | - Thomas Brabbs
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Alina Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Katherine Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Todd Richmond
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA
| | - Sukhwinder Singh
- CIMMYT, Calle Dr Norman E Borlaug, Ciudad Obregon, 85208, Mexico
| | - Leah Catchpole
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| |
Collapse
|
1427
|
Scheben A, Verpaalen B, Lawley CT, Chan CKK, Bayer PE, Batley J, Edwards D. CropSNPdb: a database of SNP array data for Brassica crops and hexaploid bread wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:142-152. [PMID: 30548723 DOI: 10.1111/tpj.14194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 05/23/2023]
Abstract
Advances in sequencing technology have led to a rapid rise in the genomic data available for plants, driving new insights into the evolution, domestication and improvement of crops. Single nucleotide polymorphisms (SNPs) are a major component of crop genomic diversity, and are invaluable as genetic markers in research and breeding programs. High-throughput SNP arrays, or 'SNP chips', can generate reproducible sets of informative SNP markers and have been broadly adopted. Although there are many public repositories for sequencing data, which are routinely uploaded, there are no formal repositories for crop SNP array data. To make SNP array data more easily accessible, we have developed CropSNPdb (http://snpdb.appliedbioinformatics.com.au), a database for SNP array data produced by the Illumina Infinium™ hexaploid bread wheat (Triticum aestivum) 90K and Brassica 60K arrays. We currently host SNPs from datasets covering 526 Brassica lines and 309 bread wheat lines, and provide search, download and upload utilities for users. CropSNPdb provides a useful repository for these data, which can be applied for a range of genomics and molecular crop-breeding activities.
Collapse
Affiliation(s)
- Armin Scheben
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Brent Verpaalen
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | | | - Chon-Kit K Chan
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
- Australian Genome Research Facility, Melbourne, Vic., 3000, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| |
Collapse
|
1428
|
Maryenti T, Kato N, Ichikawa M, Okamoto T. Establishment of an In Vitro Fertilization System in Wheat (Triticum aestivum L.). PLANT & CELL PHYSIOLOGY 2019; 60:835-843. [PMID: 30605551 DOI: 10.1093/pcp/pcy250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 12/21/2018] [Indexed: 05/11/2023]
Abstract
In vitro fertilization (IVF) systems using isolated gametes have been utilized to dissect post-fertilization events in angiosperms, since the female gametophytes of plants are deeply embedded within ovaries. In addition, IVF systems have been used to produce hybrid and polyploid zygotes. Complete IVF systems have been established in maize and rice, two of three major crop species providing the majority of human energy intake. Among those crop species, gametes of wheat have not been used to establish a complete IVF system successfully. In this study, a wheat IVF system was developed to introduce the advantages of this technology to wheat research. Fusion of gametes was performed via a modified electrofusion method, and the fusion product, a zygote, formed a cell wall and two nucleoli. The first division of zygotes was observed 19-27 h after fusion, and the resulting two-celled embryo developed into 10-20-celled globular-like embryos and multicellular club-shaped embryos by 3 and 7-10 d after fusion, respectively. Such zygotic division profiles were mostly consistent with those in the embryo sac, suggesting that the division profile of IVF-produced early embryos reflects that of early embryos in planta. Although the IVF-produced club-shaped embryos did not develop into differentiated embryos but into compact embryonic calli, fertile plants could be regenerated from the embryonic calli, and the seeds harvested from those plants grew normally into seedlings. The IVF system described here might become an important technique for generating new genotypes of wheat and/or new hybrids as well as for investigating fertilization-induced events in wheat.
Collapse
Affiliation(s)
- Tety Maryenti
- Department of Biological Sciences, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji, Tokyo, Japan
| | - Norio Kato
- Department of Biological Sciences, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji, Tokyo, Japan
- Plant Breeding Innovation Laboratory, RIKEN Cluster for Science, Tsurumi, Yokohama, Japan
- Plant Innovation Center, Japan Tobacco Inc., Higashihara 700, Iwata, Shizuoka, Japan
| | - Masako Ichikawa
- Plant Innovation Center, Japan Tobacco Inc., Higashihara 700, Iwata, Shizuoka, Japan
| | - Takashi Okamoto
- Department of Biological Sciences, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji, Tokyo, Japan
- Plant Breeding Innovation Laboratory, RIKEN Cluster for Science, Tsurumi, Yokohama, Japan
| |
Collapse
|
1429
|
Krasileva KV. The role of transposable elements and DNA damage repair mechanisms in gene duplications and gene fusions in plant genomes. CURRENT OPINION IN PLANT BIOLOGY 2019; 48:18-25. [PMID: 30849712 DOI: 10.1016/j.pbi.2019.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/16/2019] [Accepted: 01/29/2019] [Indexed: 05/02/2023]
Abstract
Plant genomes are shaped by structural variation. Gene-size insertions and among most prominent events and can have significant effects on amplification of gene families as well as facilitate new gene fusions. Transposable elements as well as plant DNA repair machinery have overlapping contributions to these events, and often work in synergy. Activity of transposable elements is often lineage specific and can preferentially affect specific gene families, such as disease resistance genes. Once duplicated, genes themselves can serve templates for additional variation that can arise from non-allelic homologous recombination. Non-homologous DNA repair mechanisms contribute to additional variation and diversify the mechanisms of gene movement, such as through ligation of extra-chromosomal DNA fragments. Genomic processes that generate structural variation can be induced by stress and, therefore, can provide adaptive potential. This review describes mechanisms that contribute to gene-size structural variation in plants, result in gene duplication and generation of new plant genes through gene fusion.
Collapse
Affiliation(s)
- Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States.
| |
Collapse
|
1430
|
Janáková E, Jakobson I, Peusha H, Abrouk M, Škopová M, Šimková H, Šafář J, Vrána J, Doležel J, Järve K, Valárik M. Divergence between bread wheat and Triticum militinae in the powdery mildew resistance QPm.tut-4A locus and its implications for cloning of the resistance gene. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1061-1072. [PMID: 30535646 PMCID: PMC6449310 DOI: 10.1007/s00122-018-3259-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/03/2018] [Indexed: 06/09/2023]
Abstract
A segment of Triticum militinae chromosome 7G harbors a gene(s) conferring powdery mildew resistance which is effective at both the seedling and the adult plant stages when transferred into bread wheat (T. aestivum). The introgressed segment replaces a piece of wheat chromosome arm 4AL. An analysis of segregating materials generated to positionally clone the gene highlighted that in a plant heterozygous for the introgression segment, only limited recombination occurs between the introgressed region and bread wheat 4A. Nevertheless, 75 genetic markers were successfully placed within the region, thereby confining the gene to a 0.012 cM window along the 4AL arm. In a background lacking the Ph1 locus, the localized rate of recombination was raised 33-fold, enabling the reduction in the length of the region containing the resistance gene to a 480 kbp stretch harboring 12 predicted genes. The substituted segment in the reference sequence of bread wheat cv. Chinese Spring is longer (640 kbp) and harbors 16 genes. A comparison of the segments' sequences revealed a high degree of divergence with respect to both their gene content and nucleotide sequence. Of the 12 T. militinae genes, only four have a homolog in cv. Chinese Spring. Possible candidate genes for the resistance have been identified based on function predicted from their sequence.
Collapse
Affiliation(s)
- Eva Janáková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Irena Jakobson
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 19086, Tallinn, Estonia
| | - Hilma Peusha
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 19086, Tallinn, Estonia
| | - Michael Abrouk
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Monika Škopová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
- Limagrain Central Europe Cereals, s.r.o., Hrubčice 111, 79821, Bedihošť, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Kadri Järve
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 19086, Tallinn, Estonia
| | - Miroslav Valárik
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic.
| |
Collapse
|
1431
|
Gardiner LJ, Brabbs T, Akhunov A, Jordan K, Budak H, Richmond T, Singh S, Catchpole L, Akhunov E, Hall A. Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat. Gigascience 2019. [PMID: 30715311 DOI: 10.5524/100554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Whole-genome shotgun resequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome, making it difficult to unambiguously assign variation. Resequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented complementary DNA/exon or gene-based probe sets in which the promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. RESULTS We present and validate 2 gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high-confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low-confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for single-nucleotide polymorphism calling while significantly reducing cost per sample for gene and putative promoter capture. CONCLUSIONS We show that a capture design employing an "island strategy" can enable analysis of the large gene/putative promoter space of wheat with only 2 × 160 Mbp probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.
Collapse
Affiliation(s)
- Laura-Jayne Gardiner
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
- IBM Research, The Hartree Centre STFC Laboratory, Sci-Tech Daresbury, Warrington, WA4 4AD, UK
| | - Thomas Brabbs
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Alina Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Katherine Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Todd Richmond
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA
| | - Sukhwinder Singh
- CIMMYT, Calle Dr Norman E Borlaug, Ciudad Obregon, 85208, Mexico
| | - Leah Catchpole
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| |
Collapse
|
1432
|
Kersey PJ. Plant genome sequences: past, present, future. CURRENT OPINION IN PLANT BIOLOGY 2019; 48:1-8. [PMID: 30579050 DOI: 10.1016/j.pbi.2018.11.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 05/19/2023]
Abstract
The green plants (Viridiplantae) are an essential kingdom of life, responsible via photosynthesis for the majority of global primary production, and directly utilized by humankind for nutrition, animal feed, fuel, clothing, medicine and other purposes. There are an estimated 391 000 species of land plants, in addition to 8000 species of green algae. Their genomes are unusually diverse compared to those of other kingdoms, ranging in size from ∼10 Mb to over 100 Gb. Knowledge of plant genomes initially lagged behind those of other kingdoms but has greatly increased with the development of new technologies for DNA sequencing; bioinformatic analysis, rather than data production, is increasingly the bottleneck to further knowledge. Recent proposals are now contemplating the sequencing, assembly and annotation of the genomes of all of the world's plant species; meanwhile, low coverage sequencing to measure diversity across collections and wild populations has already become commonplace for many species, especially those utilized as crops.
Collapse
|
1433
|
Assessing the genetic diversity and characterizing genomic regions conferring Tan Spot resistance in cultivated rye. PLoS One 2019; 14:e0214519. [PMID: 30921415 PMCID: PMC6438500 DOI: 10.1371/journal.pone.0214519] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 03/14/2019] [Indexed: 11/19/2022] Open
Abstract
Rye (Secale cereale L.) is known for its wide adaptation due to its ability to tolerate harsh environments in semiarid areas. To assess the diversity in rye we genotyped a panel of 178 geographically diverse accessions of four Secale sp. from U.S. National Small Grains Collection using 4,037 high-quality SNPs (single nucleotide polymorphisms) developed by genotyping-by-sequencing (GBS). PCA and STRUCTURE analysis revealed three major clusters that separate S. cereale L. from S. strictum and S. sylvestre, however, genetic clusters did not correlate with geographic origins and growth habit (spring/winter). The panel was evaluated for response to Pyrenophora tritici-repentis race 5 (PTR race 5) and nearly 59% accessions showed resistance or moderate resistance. Genome-wide association study (GWAS) was performed on S. cereale subsp. cereale using the 4,037 high-quality SNPs. Two QTLs (QTs.sdsu-5R and QTs.sdsu-2R) on chromosomes 5R and 2R were identified conferring resistance to PTR race 5 (p < 0.001) that explained 13.1% and 11.6% of the phenotypic variation, respectively. Comparative analysis showed a high degree of synteny between rye and wheat with known rearrangements as expected. QTs.sdsu-2R was mapped in the genomic region corresponding to wheat chromosome group 2 and QTs.sdsu-5R was mapped to a small terminal region on chromosome 4BL. Based on the genetic diversity, a set of 32 accessions was identified to represents more than 99% of the allelic diversity with polymorphic information content (PIC) of 0.25. This set can be utilized for genetic characterization of useful traits and genetic improvement of rye, triticale, and wheat.
Collapse
|
1434
|
de Haro LA, Arellano SM, Novák O, Feil R, Dumón AD, Mattio MF, Tarkowská D, Llauger G, Strnad M, Lunn JE, Pearce S, Figueroa CM, del Vas M. Mal de Río Cuarto virus infection causes hormone imbalance and sugar accumulation in wheat leaves. BMC PLANT BIOLOGY 2019; 19:112. [PMID: 30902042 PMCID: PMC6431059 DOI: 10.1186/s12870-019-1709-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/11/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Mal de Río Cuarto virus (MRCV) infects several monocotyledonous species including maize and wheat. Infected plants show shortened internodes, partial sterility, increased tillering and reduced root length. To better understand the molecular basis of the plant-virus interactions leading to these symptoms, we combined RNA sequencing with metabolite and hormone measurements. RESULTS More than 3000 differentially accumulated transcripts (DATs) were detected in MRCV-infected wheat plants at 21 days post inoculation compared to mock-inoculated plants. Infected plants exhibited decreased levels of TaSWEET13 transcripts, which are involved in sucrose phloem loading. Soluble sugars, starch, trehalose 6-phosphate (Tre6P), and organic and amino acids were all higher in MRCV-infected plants. In addition, several transcripts related to plant hormone metabolism, transport and signalling were increased upon MRCV infection. Transcripts coding for GA20ox, D14, MAX2 and SMAX1-like proteins involved in gibberellin biosynthesis and strigolactone signalling, were reduced. Transcripts involved in jasmonic acid, ethylene and brassinosteroid biosynthesis, perception and signalling and in auxin transport were also altered. Hormone measurements showed that jasmonic acid, brassinosteroids, abscisic acid and indole-3-acetic acid were significantly higher in infected leaves. CONCLUSIONS Our results indicate that MRCV causes a profound hormonal imbalance that, together with alterations in sugar partitioning, could account for the symptoms observed in MRCV-infected plants.
Collapse
Affiliation(s)
| | - Sofía Maité Arellano
- Instituto de Biotecnología, CICVyA, INTA, CONICET, Hurlingham, Buenos Aires Argentina
| | - Ondrej Novák
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany Czech Academy of Sciences, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | | | - Danuše Tarkowská
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany Czech Academy of Sciences, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Gabriela Llauger
- Instituto de Biotecnología, CICVyA, INTA, CONICET, Hurlingham, Buenos Aires Argentina
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany Czech Academy of Sciences, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - John Edward Lunn
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO USA
| | | | - Mariana del Vas
- Instituto de Biotecnología, CICVyA, INTA, CONICET, Hurlingham, Buenos Aires Argentina
| |
Collapse
|
1435
|
Moelling K, Broecker F. Viruses and Evolution - Viruses First? A Personal Perspective. Front Microbiol 2019; 10:523. [PMID: 30941110 PMCID: PMC6433886 DOI: 10.3389/fmicb.2019.00523] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 02/28/2019] [Indexed: 01/08/2023] Open
Abstract
The discovery of exoplanets within putative habitable zones revolutionized astrobiology in recent years. It stimulated interest in the question about the origin of life and its evolution. Here, we discuss what the roles of viruses might have been at the beginning of life and during evolution. Viruses are the most abundant biological entities on Earth. They are present everywhere, in our surrounding, the oceans, the soil and in every living being. Retroviruses contributed to about half of our genomic sequences and to the evolution of the mammalian placenta. Contemporary viruses reflect evolution ranging from the RNA world to the DNA-protein world. How far back can we trace their contribution? Earliest replicating and evolving entities are the ribozymes or viroids fulfilling several criteria of life. RNA can perform many aspects of life and influences our gene expression until today. The simplest structures with non-protein-coding information may represent models of life built on structural, not genetic information. Viruses today are obligatory parasites depending on host cells. Examples of how an independent lifestyle might have been lost include mitochondria, chloroplasts, Rickettsia and others, which used to be autonomous bacteria and became intracellular parasites or endosymbionts, thereby losing most of their genes. Even in vitro the loss of genes can be recapitulated all the way from coding to non-coding RNA. Furthermore, the giant viruses may indicate that there is no sharp border between living and non-living entities but an evolutionary continuum. Here, it is discussed how viruses can lose and gain genes, and that they are essential drivers of evolution. This discussion may stimulate the thinking about viruses as early possible forms of life. Apart from our view “viruses first”, there are others such as “proteins first” and “metabolism first.”
Collapse
Affiliation(s)
- Karin Moelling
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Felix Broecker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| |
Collapse
|
1436
|
Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. Nat Genet 2019; 51:739-748. [PMID: 30886425 DOI: 10.1038/s41588-019-0371-5] [Citation(s) in RCA: 435] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 02/11/2019] [Indexed: 11/08/2022]
Abstract
Allotetraploid cotton is an economically important natural-fiber-producing crop worldwide. After polyploidization, Gossypium hirsutum L. evolved to produce a higher fiber yield and to better survive harsh environments than Gossypium barbadense, which produces superior-quality fibers. The global genetic and molecular bases for these interspecies divergences were unknown. Here we report high-quality de novo-assembled genomes for these two cultivated allotetraploid species with pronounced improvement in repetitive-DNA-enriched centromeric regions. Whole-genome comparative analyses revealed that species-specific alterations in gene expression, structural variations and expanded gene families were responsible for speciation and the evolutionary history of these species. These findings help to elucidate the evolution of cotton genomes and their domestication history. The information generated not only should enable breeders to improve fiber quality and resilience to ever-changing environmental conditions but also can be translated to other crops for better understanding of their domestication history and use in improvement.
Collapse
|
1437
|
Liu Y, El-Kassaby YA. Novel Insights into Plant Genome Evolution and Adaptation as Revealed through Transposable Elements and Non-Coding RNAs in Conifers. Genes (Basel) 2019; 10:genes10030228. [PMID: 30889931 PMCID: PMC6470726 DOI: 10.3390/genes10030228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 01/03/2023] Open
Abstract
Plant genomes are punctuated by repeated bouts of proliferation of transposable elements (TEs), and these mobile bursts are followed by silencing and decay of most of the newly inserted elements. As such, plant genomes reflect TE-related genome expansion and shrinkage. In general, these genome activities involve two mechanisms: small RNA-mediated epigenetic repression and long-term mutational decay and deletion, that is, genome-purging. Furthermore, the spatial relationships between TE insertions and genes are an important force in shaping gene regulatory networks, their downstream metabolic and physiological outputs, and thus their phenotypes. Such cascading regulations finally set up a fitness differential among individuals. This brief review demonstrates factual evidence that unifies most updated conceptual frameworks covering genome size, architecture, epigenetic reprogramming, and gene expression. It aims to give an overview of the impact that TEs may have on genome and adaptive evolution and to provide novel insights into addressing possible causes and consequences of intimidating genome sizes (20⁻30 Gb) in a taxonomic group, conifers.
Collapse
Affiliation(s)
- Yang Liu
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada.
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada.
| |
Collapse
|
1438
|
Kumar A, Kapoor P, Chunduri V, Sharma S, Garg M. Potential of Aegilops sp. for Improvement of Grain Processing and Nutritional Quality in Wheat ( Triticum aestivum). FRONTIERS IN PLANT SCIENCE 2019; 10:308. [PMID: 30936886 PMCID: PMC6431632 DOI: 10.3389/fpls.2019.00308] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
Wheat is one of the most important staple crops in the world and good source of calories and nutrition. Its flour and dough have unique physical properties and can be processed to make unique products like bread, cakes, biscuits, pasta, noodles etc., which is not possible from other staple crops. Due to domestication, the genetic variability of the genes coding for different economically important traits in wheat is narrow. This genetic variability can be increased by utilizing its wild relatives. Its closest relative, genus Aegilops can be an important source of new alleles. Aegilops has played a very important role in evolution of tetraploid and hexaploid wheat. It consists of 22 species with C, D, M, N, S, T and U genomes with high allelic diversity relative to wheat. Its utilization for wheat improvement for various abiotic and biotic stresses has been reported by various scientific publications. Here in, for the first time, we review the potential of Aegilops for improvement of processing and nutritional traits in wheat. Among processing quality related gluten proteins; high molecular weight glutenins (HMW GS), being easiest to study have been explored in highest number of accessions or lines i.e., 681 belonging to 13 species and selected ones like Ae. searsii, Ae. geniculata and Ae. longissima have been linked with improved bread making quality of wheat. Gliadins and low molecular weight glutenins (LMW GS) have also been extensively explored for wheat improvement and Ae. umbellulata specific LMW GS have been linked with wheat bread making quality improvement. Aegilops has been explored for seed texture diversity and proteins like puroindolins (Pin) and grain softness proteins (GSP). For nutrition quality improvement, it has been screened for essential micronutrients like Fe, Zn, phytochemicals like carotenoids and dietary fibers like arabinoxylan and β-glucan. Ae. kotschyi and Ae. biuncialis transfer in wheat have been associated with higher Fe, Zn content. In this article we have tried to compile information available on exploration of nutritional and processing quality related traits in Aegilops section and their utilization for wheat improvement by different approaches.
Collapse
|
1439
|
Genetic Modification for Wheat Improvement: From Transgenesis to Genome Editing. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6216304. [PMID: 30956982 PMCID: PMC6431451 DOI: 10.1155/2019/6216304] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/08/2019] [Accepted: 02/21/2019] [Indexed: 12/12/2022]
Abstract
To feed the growing human population, global wheat yields should increase to approximately 5 tonnes per ha from the current 3.3 tonnes by 2050. To reach this goal, existing breeding practices must be complemented with new techniques built upon recent gains from wheat genome sequencing, and the accumulated knowledge of genetic determinants underlying the agricultural traits responsible for crop yield and quality. In this review we primarily focus on the tools and techniques available for accessing gene functions which lead to clear phenotypes in wheat. We provide a view of the development of wheat transformation techniques from a historical perspective, and summarize how techniques have been adapted to obtain gain-of-function phenotypes by gene overexpression, loss-of-function phenotypes by expressing antisense RNAs (RNA interference or RNAi), and most recently the manipulation of gene structure and expression using site-specific nucleases, such as CRISPR/Cas9, for genome editing. The review summarizes recent successes in the application of wheat genetic manipulation to increase yield, improve nutritional and health-promoting qualities in wheat, and enhance the crop's resistance to various biotic and abiotic stresses.
Collapse
|
1440
|
A Low Resolution Epistasis Mapping Approach To Identify Chromosome Arm Interactions in Allohexaploid Wheat. G3-GENES GENOMES GENETICS 2019; 9:675-684. [PMID: 30455184 PMCID: PMC6404624 DOI: 10.1534/g3.118.200646] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Epistasis is an important contributor to genetic variance. In inbred populations, pairwise epistasis is present as additive by additive interactions. Testing for epistasis presents a multiple testing problem as the pairwise search space for modest numbers of markers is large. Single markers do not necessarily track functional units of interacting chromatin as well as haplotype based methods do. To harness the power of multiple markers while minimizing the number of tests conducted, we present a low resolution test for epistatic interactions across whole chromosome arms. Epistasis covariance matrices were constructed from the additive covariances of individual chromosome arms. These covariances were subsequently used to estimate an epistatic variance parameter while correcting for background additive and epistatic effects. We find significant epistasis for 2% of the interactions tested for four agronomic traits in a winter wheat breeding population. Interactions across homeologous chromosome arms were identified, but were less abundant than other chromosome arm pair interactions. The homeologous chromosome arm pair 4BL/4DL showed a strong negative relationship between additive and interaction effects that may be indicative of functional redundancy. Several chromosome arms appeared to act as hubs in an interaction network, suggesting that they may contain important regulatory factors. The differential patterns of epistasis across different traits demonstrate that detection of epistatic interactions is robust when correcting for background additive and epistatic effects in the population. The low resolution epistasis mapping method presented here identifies important epistatic interactions with a limited number of statistical tests at the cost of low precision.
Collapse
|
1441
|
Prediction of Subgenome Additive and Interaction Effects in Allohexaploid Wheat. G3-GENES GENOMES GENETICS 2019; 9:685-698. [PMID: 30455185 PMCID: PMC6404612 DOI: 10.1534/g3.118.200613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Whole genome duplications have played an important role in the evolution of angiosperms. These events often occur through hybridization between closely related species, resulting in an allopolyploid with multiple subgenomes. With the availability of affordable genotyping and a reference genome to locate markers, breeders of allopolyploids now have the opportunity to manipulate subgenomes independently. This also presents a unique opportunity to investigate epistatic interactions between homeologous orthologs across subgenomes. We present a statistical framework for partitioning genetic variance to the subgenomes of an allopolyploid, predicting breeding values for each subgenome, and determining the importance of inter-genomic epistasis. We demonstrate using an allohexaploid wheat breeding population evaluated in Ithaca, NY and an important wheat dataset from CIMMYT previously shown to demonstrate non-additive genetic variance. Subgenome covariance matrices were constructed and used to calculate subgenome interaction covariance matrices for variance component estimation and genomic prediction. We propose a method to extract population structure from all subgenomes at once before covariances are calculated to reduce collinearity between subgenome estimates. Variance parameter estimation was shown to be reliable for additive subgenome effects, but was less reliable for subgenome interaction components. Predictive ability was equivalent to current genomic prediction methods. Including only inter-genomic interactions resulted in the same increase in accuracy as modeling all pairwise marker interactions. Thus, we provide a new tool for breeders of allopolyploid crops to characterize the genetic architecture of existing populations, determine breeding goals, and develop new strategies for selection of additive effects and fixation of inter-genomic epistasis.
Collapse
|
1442
|
Guérin C, Roche J, Allard V, Ravel C, Mouzeyar S, Bouzidi MF. Genome-wide analysis, expansion and expression of the NAC family under drought and heat stresses in bread wheat (T. aestivum L.). PLoS One 2019; 14:e0213390. [PMID: 30840709 PMCID: PMC6402696 DOI: 10.1371/journal.pone.0213390] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/19/2019] [Indexed: 02/01/2023] Open
Abstract
The NAC family is one of the largest plant-specific transcription factor families, and some of its members are known to play major roles in plant development and response to biotic and abiotic stresses. Here, we inventoried 488 NAC members in bread wheat (Triticum aestivum). Using the recent release of the wheat genome (IWGS RefSeq v1.0), we studied duplication events focusing on genomic regions from 4B-4D-5A chromosomes as an example of the family expansion and neofunctionalization of TaNAC members. Differentially expressed TaNAC genes in organs and in response to abiotic stresses were identified using publicly available RNAseq data. Expression profiling of 23 selected candidate TaNAC genes was studied in leaf and grain from two bread wheat genotypes at two developmental stages in field drought conditions and revealed insights into their specific and/or overlapping expression patterns. This study showed that, of the 23 TaNAC genes, seven have a leaf-specific expression and five have a grain-specific expression. In addition, the grain-specific genes profiles in response to drought depend on the genotype. These genes may be considered as potential candidates for further functional validation and could present an interest for crop improvement programs in response to climate change. Globally, the present study provides new insights into evolution, divergence and functional analysis of NAC gene family in bread wheat.
Collapse
Affiliation(s)
- Claire Guérin
- UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Université Clermont Auvergne, INRA, Clermont–Ferrand, France
| | - Jane Roche
- UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Université Clermont Auvergne, INRA, Clermont–Ferrand, France
- * E-mail:
| | - Vincent Allard
- UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Université Clermont Auvergne, INRA, Clermont–Ferrand, France
| | - Catherine Ravel
- UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Université Clermont Auvergne, INRA, Clermont–Ferrand, France
| | - Said Mouzeyar
- UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Université Clermont Auvergne, INRA, Clermont–Ferrand, France
| | - Mohamed Fouad Bouzidi
- UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Université Clermont Auvergne, INRA, Clermont–Ferrand, France
| |
Collapse
|
1443
|
Muqaddasi QH, Zhao Y, Rodemann B, Plieske J, Ganal MW, Röder MS. Genome-wide Association Mapping and Prediction of Adult Stage Septoria tritici Blotch Infection in European Winter Wheat via High-Density Marker Arrays. THE PLANT GENOME 2019; 12:180029. [PMID: 30951099 DOI: 10.3835/plantgenome2018.05.0029] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
blotch (STB) caused by the fungus is a devastating foliar disease of wheat ( L.) that can lead to substantial yield losses. Quantitative genetic resistance has been proposed as a durable strategy for STB control. In this study, we dissected the genetic basis of STB infection in 371 European wheat varieties based on 35k and 90k single nucleotide polymorphism marker arrays. The phenotypic data analyses suggested that large genetic variance exists for STB infection with a broad-sense heritability of 0.78. Genome-wide association studies (GWAS) propose the highly quantitative nature of STB infection with potential associations on chromosomes 1A, 1B, 2D, 4A, 5A, 6A, 6D, 7A, and 7B. Increased marker density in GWAS by combining markers from both arrays helped to detect additional markers explaining increased genotypic variance. Linkage disequilibrium analyses revealed genes with a possible role in disease resistance. The potential of genomic prediction (GP) assessed via two models accounting for additive effects and additive plus epistatic interactions among the loci suggested the possibility of genomic selection for improved STB resistance. Genomic prediction results also indicated that the higher-order epistatic interactions are not abundant and that both marker platforms are equally suitable for GP of STB infection. Our results provide further understanding of the quantitative genetic nature of STB infection, serve as a resource for marker-assisted breeding, and highlight the potential of genomic selection for improved STB resistance.
Collapse
|
1444
|
Jiang L, Sun L, Ye M, Wang J, Wang Y, Bogard M, Lacaze X, Fournier A, Beauchêne K, Gouache D, Wu R. Functional mapping of N deficiency‐induced response in wheat yield‐component traits by implementing high‐throughput phenotyping. THE PLANT JOURNAL 2019; 97:1105-1119. [PMID: 30536457 DOI: 10.1111/tpj.14186] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/09/2018] [Accepted: 11/23/2018] [Indexed: 05/25/2023]
Affiliation(s)
- Libo Jiang
- Center for Computational Biology College of Biological Sciences and Technology Beijing Forestry University Beijing 100083 China
| | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding National Engineering Research Center for Floriculture College of Landscape Architecture Beijing Forestry University Beijing 100083 China
| | - Meixia Ye
- Center for Computational Biology College of Biological Sciences and Technology Beijing Forestry University Beijing 100083 China
| | - Jing Wang
- Center for Computational Biology College of Biological Sciences and Technology Beijing Forestry University Beijing 100083 China
| | - Yaqun Wang
- Department of Biostatistics Rutgers University New Brunswick NJ 08901 USA
| | - Matthieu Bogard
- Arvalis Institut du Végétal 3‐5 Rue Joseph et Marie Hackin 75116 Paris France
| | - Xavier Lacaze
- Arvalis Institut du Végétal 3‐5 Rue Joseph et Marie Hackin 75116 Paris France
| | - Antoine Fournier
- Arvalis Institut du Végétal 3‐5 Rue Joseph et Marie Hackin 75116 Paris France
| | - Katia Beauchêne
- Arvalis Institut du Végétal 3‐5 Rue Joseph et Marie Hackin 75116 Paris France
| | - David Gouache
- Arvalis Institut du Végétal 3‐5 Rue Joseph et Marie Hackin 75116 Paris France
| | - Rongling Wu
- Center for Computational Biology College of Biological Sciences and Technology Beijing Forestry University Beijing 100083 China
- Center for Statistical Genetics Departments of Public Health Sciences and Statistics Pennsylvania State University Hershey PA 17033 USA
| |
Collapse
|
1445
|
Gabur I, Chawla HS, Snowdon RJ, Parkin IAP. Connecting genome structural variation with complex traits in crop plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:733-750. [PMID: 30448864 DOI: 10.1007/s00122-018-3233-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/07/2018] [Indexed: 05/05/2023]
Abstract
Structural genome variation is a major determinant of useful trait diversity. We describe how genome analysis methods are enabling discovery of trait-associated structural variants and their potential impact on breeding. As our understanding of complex crop genomes continues to grow, there is growing evidence that structural genome variation plays a major role in determining traits important for breeding and agriculture. Identifying the extent and impact of structural variants in crop genomes is becoming increasingly feasible with ongoing advances in the sophistication of genome sequencing technologies, particularly as it becomes easier to generate accurate long sequence reads on a genome-wide scale. In this article, we discuss the origins of structural genome variation in crops from ancient and recent genome duplication and polyploidization events and review high-throughput methods to assay such variants in crop populations in order to find associations with phenotypic traits. There is increasing evidence from such studies that gene presence-absence and copy number variation resulting from segmental chromosome exchanges may be at the heart of adaptive variation of crops to counter abiotic and biotic stress factors. We present examples from major crops that demonstrate the potential of pangenomic diversity as a key resource for future plant breeding for resilience and sustainability.
Collapse
Affiliation(s)
- Iulian Gabur
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Harmeet Singh Chawla
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N OX2, Canada
| |
Collapse
|
1446
|
Bettgenhaeuser J, Krattinger SG. Rapid gene cloning in cereals. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:699-711. [PMID: 30341495 DOI: 10.1007/s00122-018-3210-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/12/2018] [Indexed: 05/03/2023]
Abstract
The large and complex genomes of many cereals hindered cloning efforts in the past. Advances in genomics now allow the rapid cloning of genes from humanity's most valuable crops. The past two decades were characterized by a genomics revolution that entailed profound changes to crop research, plant breeding, and agriculture. Today, high-quality reference sequences are available for all major cereal crop species. Large resequencing and pan-genome projects start to reveal a more comprehensive picture of the genetic makeup and the diversity among domesticated cereals and their wild relatives. These technological advancements will have a dramatic effect on dissecting genotype-phenotype associations and on gene cloning. In this review, we will highlight the status of the genomic resources available for various cereal crops and we will discuss their implications for gene cloning. A particular focus will be given to the cereal species barley and wheat, which are characterized by very large and complex genomes that have been inaccessible to rapid gene cloning until recently. With the advancements in genomics and the development of several rapid gene-cloning methods, it has now become feasible to tackle the cloning of most agriculturally important genes, even in wheat and barley.
Collapse
Affiliation(s)
- Jan Bettgenhaeuser
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Simon G Krattinger
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| |
Collapse
|
1447
|
Monat C, Schreiber M, Stein N, Mascher M. Prospects of pan-genomics in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:785-796. [PMID: 30446793 DOI: 10.1007/s00122-018-3234-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/07/2018] [Indexed: 05/10/2023]
Abstract
The concept of a pan-genome refers to intraspecific diversity in genome content and structure, encompassing both genes and intergenic space. Pan-genomic studies employ a combination of de novo sequence assembly and reference-based alignment to discover and genotype structural variants. The large size and complex structure of Triticeae genomes were for a long time an obstacle for genomic research in barley and its relatives. Now that a reference genome is available, computational pipelines for high-quality sequence assembly are in place, and sequence costs continue to drop, investigations into the structural diversity of the barley genome seem within reach. Here, we review the recent progress on pan-genomics in the model grass Brachypodium distachyon, and the cereal crops rice and maize, and devise a multi-tiered strategy for a pan-genome project in barley. Our design involves: (1) the construction of high-quality de novo sequence assemblies for a small core set of representative genotypes, (2) short-read sequencing of a large diversity panel of genebank accessions to medium coverage and (3) the use of complementary methods such as chromosome-conformation capture sequencing and k-mer-based association genetics. The in silico representation of the barley pan-genome may inform about the mechanisms of structural genome evolution in the Triticeae and supplement quantitative genetics models of crop performance for better accuracy and predictive ability.
Collapse
Affiliation(s)
- Cécile Monat
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, 37075, Göttingen, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
| |
Collapse
|
1448
|
Sánchez-Martín J, Keller B. Contribution of recent technological advances to future resistance breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:713-732. [PMID: 30756126 DOI: 10.1007/s00122-019-03297-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/02/2019] [Indexed: 05/23/2023]
Abstract
The development of durable host resistance strategies to control crop diseases is a primary need for sustainable agricultural production in the future. This article highlights the potential of recent progress in the understanding of host resistance for future cereal breeding. Much of the novel work is based on advancements in large-scale sequencing and genomics, rapid gene isolation techniques and high-throughput molecular marker technologies. Moreover, emerging applications on the pathogen side like effector identification or field pathogenomics are discussed. The combination of knowledge from both sides of cereal pathosystems will result in new approaches for resistance breeding. We describe future applications and innovative strategies to implement effective and durable strategies to combat diseases of major cereal crops while reducing pesticide dependency.
Collapse
Affiliation(s)
- Javier Sánchez-Martín
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| |
Collapse
|
1449
|
Haas M, Schreiber M, Mascher M. Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:204-225. [PMID: 30414305 DOI: 10.1111/jipb.12737] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/27/2018] [Indexed: 05/02/2023]
Abstract
Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre-dates the era of next-generation sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance (relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large, complex genomes which were long thought to be beyond the scope of whole-genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors, as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.
Collapse
Affiliation(s)
- Matthew Haas
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
| | - Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| |
Collapse
|
1450
|
Cobo N, Wanjugi H, Lagudah E, Dubcovsky J. A High-Resolution Map of Wheat QYr.ucw-1BL, an Adult Plant Stripe Rust Resistance Locus in the Same Chromosomal Region as Yr29. THE PLANT GENOME 2019; 12:180055. [PMID: 30951084 DOI: 10.3835/plantgenome2018.08.0055] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The appearance of highly virulent and more aggressive races of f. sp. () during the last two decades has led to stripe rust epidemics worldwide and to the rapid erosion of effective resistance genes. In this study, we mapped an adult-plant resistance locus from the Argentinean wheat ( L.) cultivar Klein Chajá, which is effective against these new races. By using wheat exome capture data and a large population of 2480 segregating plants (4960 gametes), we mapped within a 0.24-cM region [332 kb in International Wheat Genome Sequencing Consortium (IWGSC) RefSeq version 1.0] on chromosome arm 1BL. This region overlaps with current maps of the adult-plant resistance gene , which has remained effective for more than 60 yr. An allelism test failed to find recombination between and and yielded similar resistance phenotypes for the two loci. These results, together with similar haplotypes in the candidate region, suggested that and might represent the same gene. However, we cannot rule out the possibility of tightly linked but different genes because most of the 13 genes in the candidate region are annotated with functions associated with disease resistance. To evaluate their potential as candidate genes, we characterized their polymorphisms between resistant and susceptible haplotypes. Finally, we used these polymorphisms to develop high-throughput markers to accelerate the deployment of these resistance loci in wheat breeding programs.
Collapse
|