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Geethanjali S, Kadirvel P, Periyannan S. Wheat improvement through advances in single nucleotide polymorphism (SNP) detection and genotyping with a special emphasis on rust resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:224. [PMID: 39283360 PMCID: PMC11405505 DOI: 10.1007/s00122-024-04730-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 08/24/2024] [Indexed: 09/22/2024]
Abstract
KEY MESSAGE Single nucleotide polymorphism (SNP) markers in wheat and their prospects in breeding with special reference to rust resistance. Single nucleotide polymorphism (SNP)-based markers are increasingly gaining momentum for screening and utilizing vital agronomic traits in wheat. To date, more than 260 million SNPs have been detected in modern cultivars and landraces of wheat. This rapid SNP discovery was made possible through the release of near-complete reference and pan-genome assemblies of wheat and its wild relatives, coupled with whole genome sequencing (WGS) of thousands of wheat accessions. Further, genotyping customized SNP sites were facilitated by a series of arrays (9 to 820Ks), a cost effective substitute WGS. Lately, germplasm-specific SNP arrays have been introduced to characterize novel traits and detect closely linked SNPs for marker-assisted breeding. Subsequently, the kompetitive allele-specific PCR (KASP) assay was introduced for rapid and large-scale screening of specific SNP markers. Moreover, with the advances and reduction in sequencing costs, ample opportunities arise for generating SNPs artificially through mutations and in combination with next-generation sequencing and comparative genomic analyses. In this review, we provide historical developments and prospects of SNP markers in wheat breeding with special reference to rust resistance where over 50 genetic loci have been characterized through SNP markers. Rust resistance is one of the most essential traits for wheat breeding as new strains of the Puccinia fungus, responsible for rust diseases, evolve frequently and globally.
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Affiliation(s)
- Subramaniam Geethanjali
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland, 4350, Australia
| | - Palchamy Kadirvel
- Crop Improvement Section, Indian Council of Agricultural Research-Indian Institute of Oilseeds Research, Hyderabad, Telangana, 500030, India
| | - Sambasivam Periyannan
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland, 4350, Australia.
- School of Agriculture and Environmental Science, University of Southern Queensland, Toowoomba, Queensland, 4350, Australia.
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Kolmer JA, Bajgain P, Rouse MN, Li J, Zhang P. Mapping and characterization of the recessive leaf rust resistance gene Lr83 on wheat chromosome arm 1DS. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:115. [PMID: 37083869 DOI: 10.1007/s00122-023-04361-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE The leaf rust resistance gene in Thatcher wheat derivative 78-1 was mapped to chromosome 1DS with SNP markers and designated as Lr83. 'Thatcher' wheat near isogenic line RL6149, a putative derivative of Triticum dicoccoides, was previously determined to carry leaf rust resistance gene Lr64 on chromosome arm 6AL and a second gene temporarily named LrX on chromosome arm 1DS. The objective of this study was to map and characterize LrX in a population of recombinant inbred lines (RILs) that segregated for a single gene. Thatcher line 78-1 with LrX was crossed with Thatcher and individual F2 seedlings and F6 RILs were evaluated for leaf rust response. The 208 F2 plants segregated for a single recessive gene and 148 F6 lines for a single gene. The RILs and parents were characterized by genotyping by sequencing (GBS). Six GBS markers and five Kompetitive Allele-Specific PCR (KASP) markers were used to map LrX on the distal region of chromosome arm 1DS. LrX was 1 centiMorgan (cM) proximal to marker K-IWB38437 and 0.4 cM distal to GBS marker 1D_9037138. Line 78-1 was crossed with Thatcher wheat lines with Lr21, Lr42, and Lr60 for allelism tests. LrX mapped 19.49 cM from Lr21 and 11.93 cM from Lr42. In the cross of line 78-1 with the Thatcher line with Lr60, one recombinant in 1,003 F2 plants was found. LrX and Lr60 are at tightly linked loci on the distal region of chromosome arm 1DS. The gene in line 78-1 was designated as Lr83. Cytological examination of RL6149 provided no evidence of transfer of a chromosome segment of an A- or B-genome chromosome to chromosome 1D.
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Affiliation(s)
- J A Kolmer
- United States Department of Agriculture - Agricultural Research Service, Cereal Disease Laboratory, Saint Paul, MN, 55108, USA.
| | - P Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - M N Rouse
- United States Department of Agriculture - Agricultural Research Service, Cereal Disease Laboratory, Saint Paul, MN, 55108, USA
| | - J Li
- School of Life and Environmental Sciences, Plant Breeding Institute, University of Sydney, Cobbitty, NSW, 2570, Australia
| | - P Zhang
- School of Life and Environmental Sciences, Plant Breeding Institute, University of Sydney, Cobbitty, NSW, 2570, Australia
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3
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Kou H, Zhang Z, Yang Y, Wei C, Xu L, Zhang G. Advances in the Mining of Disease Resistance Genes from Aegilops tauschii and the Utilization in Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12040880. [PMID: 36840228 PMCID: PMC9966637 DOI: 10.3390/plants12040880] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 06/02/2023]
Abstract
Aegilops tauschii is one of the malignant weeds that affect wheat production and is also the wild species ancestor of the D genome of hexaploid wheat (Triticum aestivum, AABBDD). It contains many disease resistance genes that have been lost in the long-term evolution of wheat and is an important genetic resource for the mining and utilization of wheat disease resistance genes. In recent years, the genome sequence of Aegilops tauschii has been preliminarily completed, which has laid a good foundation for the further exploration of wheat disease resistance genes in Aegilops tauschii. There are many studies on disease resistance genes in Aegilops tauschii; in order to provide better help for the disease resistance breeding of wheat, this paper analyzes and reviews the relationship between Aegilops tauschii and wheat, the research progress of Aegilops tauschii, the discovery of disease resistance genes from Aegilops tauschii, and the application of disease resistance genes from Aegilops tauschii to modern wheat breeding, providing a reference for the further exploration and utilization of Aegilops tauschii in wheat disease resistance breeding.
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Affiliation(s)
- Hongyun Kou
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
| | - Zhenbo Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
| | - Yu Yang
- College of Agriculture and Bioengineering, Heze University, Heze 274015, China
| | - Changfeng Wei
- College of Agriculture and Bioengineering, Heze University, Heze 274015, China
| | - Lili Xu
- College of Agriculture and Bioengineering, Heze University, Heze 274015, China
| | - Guangqiang Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Agriculture and Bioengineering, Heze University, Heze 274015, China
- Shandong Shofine Seed Technology Co., Ltd., Jining 272400, China
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Kaur S, Gill HS, Breiland M, Kolmer JA, Gupta R, Sehgal SK, Gill U. Identification of leaf rust resistance loci in a geographically diverse panel of wheat using genome-wide association analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1090163. [PMID: 36818858 PMCID: PMC9929074 DOI: 10.3389/fpls.2023.1090163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Leaf rust, caused by Puccinia triticina (Pt) is among the most devastating diseases posing a significant threat to global wheat production. The continuously evolving virulent Pt races in North America calls for exploring new sources of leaf rust resistance. A diversity panel of 365 bread wheat accessions selected from a worldwide population of landraces and cultivars was evaluated at the seedling stage against four Pt races (TDBJQ, TBBGS, MNPSD and, TNBJS). A wide distribution of seedling responses against the four Pt races was observed. Majority of the genotypes displayed a susceptible response with only 28 (9.8%), 59 (13.5%), 45 (12.5%), and 29 (8.1%) wheat accessions exhibiting a highly resistant response to TDBJQ, TBBGS, MNPSD and, TNBJS, respectively. Further, we conducted a high-resolution multi-locus genome-wide association study (GWAS) using a set of 302,524 high-quality single nucleotide polymorphisms (SNPs). The GWAS analysis identified 27 marker-trait associations (MTAs) for leaf rust resistance on different wheat chromosomes of which 20 MTAs were found in the vicinity of known Lr genes, MTAs, or quantitative traits loci (QTLs) identified in previous studies. The remaining seven significant MTAs identified represent genomic regions that harbor potentially novel genes for leaf rust resistance. Furthermore, the candidate gene analysis for the significant MTAs identified various genes of interest that may be involved in disease resistance. The identified resistant lines and SNPs linked to the QTLs in this study will serve as valuable resources in wheat rust resistance breeding programs.
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Affiliation(s)
- Shivreet Kaur
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Harsimardeep S. Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Matthew Breiland
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - James A. Kolmer
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN, United States
| | - Rajeev Gupta
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fargo, ND, United States
| | - Sunish K. Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Upinder Gill
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
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Gill HS, Halder J, Zhang J, Rana A, Kleinjan J, Amand PS, Bernardo A, Bai G, Sehgal SK. Whole-genome analysis of hard winter wheat germplasm identifies genomic regions associated with spike and kernel traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2953-2967. [PMID: 35939073 DOI: 10.1007/s00122-022-04160-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Genetic dissection of yield component traits including spike and kernel characteristics is essential for the continuous improvement in wheat yield. Genome-wide association studies (GWAS) have been frequently used to identify genetic determinants for spike and kernel-related traits in wheat, though none have been employed in hard winter wheat (HWW) which represents a major class in US wheat acreage. Further, most of these studies relied on assembled diversity panels instead of adapted breeding lines, limiting the transferability of results to practical wheat breeding. Here we assembled a population of advanced/elite breeding lines and well-adapted cultivars and evaluated over four environments for phenotypic analysis of spike and kernel traits. GWAS identified 17 significant multi-environment marker-trait associations (MTAs) for various traits, representing 12 putative quantitative trait loci (QTLs), with five QTLs affecting multiple traits. Four of these QTLs mapped on three chromosomes 1A, 5B, and 7A for spike length, number of spikelets per spike (NSPS), and kernel length are likely novel. Further, a highly significant QTL was detected on chromosome 7AS that has not been previously associated with NSPS and putative candidate genes were identified in this region. The allelic frequencies of important quantitative trait nucleotides (QTNs) were deduced in a larger set of 1,124 accessions which revealed the importance of identified MTAs in the US HWW breeding programs. The results from this study could be directly used by the breeders to select the lines with favorable alleles for making crosses, and reported markers will facilitate marker-assisted selection of stable QTLs for yield components in wheat breeding.
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Affiliation(s)
- Harsimardeep S Gill
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Jyotirmoy Halder
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Jinfeng Zhang
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Anshul Rana
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Jonathan Kleinjan
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Paul St Amand
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Amy Bernardo
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
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Zhang J, Gill HS, Halder J, Brar NK, Ali S, Bernardo A, Amand PS, Bai G, Turnipseed B, Sehgal SK. Multi-Locus Genome-Wide Association Studies to Characterize Fusarium Head Blight (FHB) Resistance in Hard Winter Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:946700. [PMID: 35958201 PMCID: PMC9359313 DOI: 10.3389/fpls.2022.946700] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/20/2022] [Indexed: 05/25/2023]
Abstract
Fusarium head blight (FHB), caused by the fungus Fusarium graminearum Schwabe is an important disease of wheat that causes severe yield losses along with serious quality concerns. Incorporating the host resistance from either wild relatives, landraces, or exotic materials remains challenging and has shown limited success. Therefore, a better understanding of the genetic basis of native FHB resistance in hard winter wheat (HWW) and combining it with major quantitative trait loci (QTLs) can facilitate the development of FHB-resistant cultivars. In this study, we evaluated a set of 257 breeding lines from the South Dakota State University (SDSU) breeding program to uncover the genetic basis of native FHB resistance in the US hard winter wheat. We conducted a multi-locus genome-wide association study (ML-GWAS) with 9,321 high-quality single-nucleotide polymorphisms (SNPs). A total of six distinct marker-trait associations (MTAs) were identified for the FHB disease index (DIS) on five different chromosomes including 2A, 2B, 3B, 4B, and 7A. Further, eight MTAs were identified for Fusarium-damaged kernels (FDK) on six chromosomes including 3B, 5A, 6B, 6D, 7A, and 7B. Out of the 14 significant MTAs, 10 were found in the proximity of previously reported regions for FHB resistance in different wheat classes and were validated in HWW, while four MTAs represent likely novel loci for FHB resistance. Accumulation of favorable alleles of reported MTAs resulted in significantly lower mean DIS and FDK score, demonstrating the additive effect of FHB resistance alleles. Candidate gene analysis for two important MTAs identified several genes with putative proteins of interest; however, further investigation of these regions is needed to identify genes conferring FHB resistance. The current study sheds light on the genetic basis of native FHB resistance in the US HWW germplasm and the resistant lines and MTAs identified in this study will be useful resources for FHB resistance breeding via marker-assisted selection.
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Affiliation(s)
- Jinfeng Zhang
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Harsimardeep S. Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Jyotirmoy Halder
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Navreet K. Brar
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Shaukat Ali
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Amy Bernardo
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Paul St. Amand
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Brent Turnipseed
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Sunish K. Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
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7
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Mourad AMI, Draz IS, Omar GE, Börner A, Esmail SM. Genome-Wide Screening of Broad-Spectrum Resistance to Leaf Rust ( Puccinia triticina Eriks) in Spring Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:921230. [PMID: 35812968 PMCID: PMC9258335 DOI: 10.3389/fpls.2022.921230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/30/2022] [Indexed: 06/01/2023]
Abstract
Wheat leaf rust (LR) causes significant yield losses worldwide. In Egypt, resistant cultivars began to lose their efficiency in leaf rust resistance. Therefore, a diverse spring wheat panel was evaluated at the seedling stage to identify new sources of broad-spectrum seedling resistance against the Egyptian Puccinia triticina (Pt) races. In three different experiments, seedling evaluation was done using Pt spores collected from different fields and growing seasons. Highly significant differences were found among experiments confirming the presence of different races population in each experiment. Highly significant differences were found among the tested genotypes confirming the ability to select superior genotypes. Genome-wide association study (GWAS) was conducted for each experiment and a set of 87 markers located within 48 gene models were identified. The identified gene models were associated with disease resistance in wheat. Five gene models were identified to resist all Pt races in at least two experiments and could be identified as stable genes under Egyptian conditions. Ten genotypes from five different countries were stable against all the tested Pt races but showed different degrees of resistance.
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Affiliation(s)
- Amira M. I. Mourad
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Ibrahim S. Draz
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Ghady E. Omar
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Samar M. Esmail
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
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8
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Lin G, Chen H, Tian B, Sehgal SK, Singh L, Xie J, Rawat N, Juliana P, Singh N, Shrestha S, Wilson DL, Shult H, Lee H, Schoen AW, Tiwari VK, Singh RP, Guttieri MJ, Trick HN, Poland J, Bowden RL, Bai G, Gill B, Liu S. Cloning of the broadly effective wheat leaf rust resistance gene Lr42 transferred from Aegilops tauschii. Nat Commun 2022; 13:3044. [PMID: 35650212 PMCID: PMC9160033 DOI: 10.1038/s41467-022-30784-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/18/2022] [Indexed: 11/09/2022] Open
Abstract
The wheat wild relative Aegilops tauschii was previously used to transfer the Lr42 leaf rust resistance gene into bread wheat. Lr42 confers resistance at both seedling and adult stages, and it is broadly effective against all leaf rust races tested to date. Lr42 has been used extensively in the CIMMYT international wheat breeding program with resulting cultivars deployed in several countries. Here, using a bulked segregant RNA-Seq (BSR-Seq) mapping strategy, we identify three candidate genes for Lr42. Overexpression of a nucleotide-binding site leucine-rich repeat (NLR) gene AET1Gv20040300 induces strong resistance to leaf rust in wheat and a mutation of the gene disrupted the resistance. The Lr42 resistance allele is rare in Ae. tauschii and likely arose from ectopic recombination. Cloning of Lr42 provides diagnostic markers and over 1000 CIMMYT wheat lines carrying Lr42 have been developed documenting its widespread use and impact in crop improvement.
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Affiliation(s)
- Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Hui Chen
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Bin Tian
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA.,Syngenta Crop Protection, Research Triangle Park, Durham, NC, 27709, USA
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57006, USA
| | - Lovepreet Singh
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Jingzhong Xie
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA.,State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Philomin Juliana
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico.,Borlaug Institute for South Asia, Ludhiana, India
| | - Narinder Singh
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA.,Bayer R&D Services LLC, Kansas City, MO, 64153, USA
| | - Sandesh Shrestha
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Duane L Wilson
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Hannah Shult
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Hyeonju Lee
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Adam William Schoen
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
| | - Mary J Guttieri
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, 66506-5502, USA
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA.,Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Robert L Bowden
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, 66506-5502, USA
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506-5502, USA.,Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, 66506-5502, USA
| | - Bikram Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA.
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA.
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9
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Volkova G, Kudinova O, Vaganova O, Agapova V. Effectiveness of Leaf Rust Resistance Genes in the Adult and Juvenile Stages in Southern Russia in 2011–2020. PLANTS 2022; 11:plants11060793. [PMID: 35336675 PMCID: PMC8953555 DOI: 10.3390/plants11060793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/12/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022]
Abstract
Puccinia triticina Erikss. is a causative agent of wheat leaf rust spread worldwide. Wheat rust is a major disease on wheat in southern regions of Russia, which are leaders in grain production and have favorable conditions for pathogen development. In this paper we studied the effectiveness of 52 NILs of cv. Thatcher with Lr genes in field trials and 41 NILs—in the juvenile phase in a greenhouse during 2011–2020. We conclude that the lines with Lr9, Lr42 and Lr43+24 genes remained immune in the adult phase during ten years of research. Lines with Lr genes: 19, 24, 29, 36, 37, 38, 43, 45, 47, 50 showed efficiency in field tests (1–5 R on the CIMMYT scale). No immune lines to Puccinia triticina were registered in the juvenile phase during 2011–2020. The line with the Lr9 gene remained immune up to 2020; Lr19 and Lr41—up to 2015; Lr42—up to 2018, and Lr50—up to 2019. In 2020, there was an increase of P. triticina isolates with virulence to Thatcher lines with Lr: 9, 14a, 16, 19, 21, 28, 30, 33, 40, 45, W, 50. Additionally, we registered a change in infection types towards more susceptible in isogenic Lr gene lines: 1, 2a, 12, 14b, 15, 18, 20, 23, 25, 28, 29, 32, 35, 36, 37, 38, 40, 44, 45 in the field. A sharp increase in the frequencies of virulent isolates was recorded in 2018–2020 due to unfavorable weather in the growing seasons. This indicates the ability of a dangerous pathogen to rapidly evolve in response to biotic and abiotic stresses. Therefore, annual monitoring of the reaction of isogenic lines, selected released varieties and the study of the virulence of the phytopathogen are important measures necessary to prevent and control leaf rust in grain-producing regions of the world.
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Xu S, Ji X, Sun S, Han H, Zhang J, Zhou S, Yang X, Li X, Li L, Liu W. Production of new wheat- A. cristatum translocation lines with modified chromosome 2P coding for powdery mildew and leaf rust resistance. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:14. [PMID: 37309409 PMCID: PMC10248630 DOI: 10.1007/s11032-022-01286-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Agropyron cristatum (L.) Gaertn. (2n = 28, PPPP), a relative of wheat, carries desirable genes associated with high yield, disease resistance, and stress resistance, which is an important resource for wheat genetic improvement. The long arm of A. cristatum chromosome 2P carries favorable genes conferring powdery mildew and leaf rust resistance, and two wheat-A. cristatum 2P translocation lines, 2PT3 and 2PT5, with a large segment of 2P chromatin were obtained. In this study, 2PT3 and 2PT5 translocation lines with powdery mildew and leaf rust resistance genes were used to induce translocations of different chromosomal sizes via ionizing radiation. According to cytological characterization, 10 of those plants were new wheat-A. cristatum 2P small-chromosome segment translocation lines with reduced 2P chromatin, and 6 plants represented introgression lines without visible 2P chromosomal fragments. Moreover, four lines were resistant to both powdery mildew and leaf rust, while two lines were resistant only to leaf rust.
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Affiliation(s)
- Shirui Xu
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiajie Ji
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Suli Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Haiming Han
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jinpeng Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shenghui Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xinming Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiuquan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lihui Li
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Weihua Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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11
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Wheat Resistance to Stripe and Leaf Rusts Conferred by Introgression of Slow Rusting Resistance Genes. J Fungi (Basel) 2021; 7:jof7080622. [PMID: 34436161 PMCID: PMC8397070 DOI: 10.3390/jof7080622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/17/2022] Open
Abstract
Twenty-three wheat genotypes were evaluated for stripe and leaf rusts, caused by Puccinia striiformis f. sp. tritici and Puccinia triticina f. sp. tritici, respectively, at seedling and adult stages under greenhouses and field conditions during the 2019/2020 and 2020/2021 growing seasons. The race analysis revealed that 250E254 and TTTST races for stripe and leaf rusts, respectively were the most aggressive. Eight wheat genotypes (Misr-3, Misr-4, Giza-171, Gemmeiza-12, Lr34/Yr18, Lr37/Yr17, Lr46/Yr29, and Lr67/Yr46) were resistant to stripe and leaf rusts at seedling and adult stages. This result was confirmed by identifying the resistance genes: Lr34/Yr18, Lr37/Yr17, Lr46/Yr29, and Lr67/Yr46 in these genotypes showing their role in the resistance. Sids-14 and Shandweel-1 genotypes were susceptible to stripe and leaf rusts. Twelve crosses between the two new susceptible wheat genotypes and the three slow rusting genes (Lr34/Yr18, Lr37/Yr17, and Lr67/Yr46) were conducted. The frequency distribution of disease severity (%) in F2 plants of the twelve crosses was ranged from 0 to 80%. Resistant F2 plants were selected and the resistance genes were detected. This study is important for introducing new active resistance genes into the breeding programs and preserving diversity among recently released wheat genotypes.
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12
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Zhang Q, Wei W, Zuansun X, Zhang S, Wang C, Liu N, Qiu L, Wang W, Guo W, Ma J, Peng H, Hu Z, Sun Q, Xie C. Fine Mapping of the Leaf Rust Resistance Gene Lr65 in Spelt Wheat 'Altgold'. FRONTIERS IN PLANT SCIENCE 2021; 12:666921. [PMID: 34262578 PMCID: PMC8274547 DOI: 10.3389/fpls.2021.666921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/04/2021] [Indexed: 06/13/2023]
Abstract
Wheat leaf rust (also known as brown rust), caused by the fungal pathogen Puccinia triticina Erikss. (Pt), is one by far the most troublesome wheat disease worldwide. The exploitation of resistance genes has long been considered as the most effective and sustainable method to control leaf rust in wheat production. Previously the leaf rust resistance gene Lr65 has been mapped to the distal end of chromosome arm 2AS linked to molecular marker Xbarc212. In this study, Lr65 was delimited to a 0.8 cM interval between flanking markers Alt-64 and AltID-11, by employing two larger segregating populations obtained from crosses of the resistant parent Altgold Rotkorn (ARK) with the susceptible parents Xuezao and Chinese Spring (CS), respectively. 24 individuals from 622 F2 plants of crosses between ARK and CS were obtained that showed the recombination between Lr65 gene and the flanking markers Alt-64 and AltID-11. With the aid of the CS reference genome sequence (IWGSC RefSeq v1.0), one SSR marker was developed between the interval matched to the Lr65-flanking marker and a high-resolution genetic linkage map was constructed. The Lr65 was finally located to a region corresponding to 60.11 Kb of the CS reference genome. The high-resolution genetic linkage map founded a solid foundation for the map-based cloning of Lr65 and the co-segregating marker will facilitate the marker-assisted selection (MAS) of the target gene.
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13
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Vitale P, Fania F, Esposito S, Pecorella I, Pecchioni N, Palombieri S, Sestili F, Lafiandra D, Taranto F, De Vita P. QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents. Genes (Basel) 2021; 12:genes12040604. [PMID: 33923933 PMCID: PMC8074140 DOI: 10.3390/genes12040604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 01/20/2023] Open
Abstract
Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F2 and F2-derived F3 families) and late (F6 and F7, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F2 and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F2 mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.
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Affiliation(s)
- Paolo Vitale
- Department of Agriculture, Food, Natural Science, Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (P.V.); (F.F.)
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Fabio Fania
- Department of Agriculture, Food, Natural Science, Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (P.V.); (F.F.)
| | - Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Ivano Pecorella
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Samuela Palombieri
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (S.P.); (F.S.); (D.L.)
| | - Francesco Sestili
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (S.P.); (F.S.); (D.L.)
| | - Domenico Lafiandra
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (S.P.); (F.S.); (D.L.)
| | - Francesca Taranto
- Institute of Biosciences and Bioresources (CNR-IBBR), 80055 Portici, Italy
- Correspondence: (F.T.); (P.D.V.)
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
- Correspondence: (F.T.); (P.D.V.)
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14
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Colasuonno P, Marcotuli I, Gadaleta A, Soriano JM. From Genetic Maps to QTL Cloning: An Overview for Durum Wheat. PLANTS (BASEL, SWITZERLAND) 2021; 10:315. [PMID: 33562160 PMCID: PMC7914919 DOI: 10.3390/plants10020315] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 12/17/2022]
Abstract
Durum wheat is one of the most important cultivated cereal crops, providing nutrients to humans and domestic animals. Durum breeding programs prioritize the improvement of its main agronomic traits; however, the majority of these traits involve complex characteristics with a quantitative inheritance (quantitative trait loci, QTL). This can be solved with the use of genetic maps, new molecular markers, phenotyping data of segregating populations, and increased accessibility to sequences from next-generation sequencing (NGS) technologies. This allows for high-density genetic maps to be developed for localizing candidate loci within a few Kb in a complex genome, such as durum wheat. Here, we review the identified QTL, fine mapping, and cloning of QTL or candidate genes involved in the main traits regarding the quality and biotic and abiotic stresses of durum wheat. The current knowledge on the used molecular markers, sequence data, and how they changed the development of genetic maps and the characterization of QTL is summarized. A deeper understanding of the trait architecture useful in accelerating durum wheat breeding programs is envisioned.
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Affiliation(s)
- Pasqualina Colasuonno
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Jose Miguel Soriano
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198 Lleida, Spain
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15
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Molecular breeding for rust resistance in wheat genotypes. Mol Biol Rep 2021; 48:731-742. [PMID: 33389532 DOI: 10.1007/s11033-020-06015-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
Rusts are a group of major diseases that have an adverse effect on crop production. Those targeting wheat are found in three principal forms: leaf, stripe, and stem rust. Leaf rust causes foliar disease in wheat; in Egypt, this causes a significant annual yield loss. The deployment of resistant genotypes has proved to be a relatively economical and environmentally sustainable method of controlling the disease. Gene pyramiding can be performed using traditional breeding techniques. Additionally, pathotypes can be introduced to examine specific leaf rust genes, or the breeder may conduct more complex breeding methods. Indirect selection via DNA markers linked to resistance genes may facilitate the transfer of targeted genes, either individually or in combination, even in a disease-free environment. The use of selective crosses to counter virulent races of leaf, stripe, and stem rust has resulted in the transfer of several resistance genes into new wheat germplasm from cultivated or wild species. Quantitative trait locus (QTL) technology has been adopted in a wide variety of novel approaches and is becoming increasingly recognized in wheat breeding. Moreover, several researchers have reported the transference of leaf and stripe rust resistance genes into susceptible wheat cultivars.
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16
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Rollar S, Serfling A, Geyer M, Hartl L, Mohler V, Ordon F. QTL mapping of adult plant and seedling resistance to leaf rust (Puccinia triticina Eriks.) in a multiparent advanced generation intercross (MAGIC) wheat population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:37-51. [PMID: 33201290 PMCID: PMC7813716 DOI: 10.1007/s00122-020-03657-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/28/2020] [Indexed: 05/22/2023]
Abstract
The Bavarian MAGIC Wheat population, comprising 394 F6:8 recombinant inbred lines was phenotyped for Puccinia triticina resistance in multi-years' field trials at three locations and in a controlled environment seedling test. Simple intervall mapping revealed 19 QTL, corresponding to 11 distinct chromosomal regions. The biotrophic rust fungus Puccinia triticina is one of the most important wheat pathogens with the potential to cause yield losses up to 70%. Growing resistant cultivars is the most cost-effective and environmentally friendly way to encounter this problem. The emergence of leaf rust races being virulent against common resistance genes increases the demand for wheat varieties with novel resistances. In the past decade, the use of complex experimental populations, like multiparent advanced generation intercross (MAGIC) populations, has risen and offers great advantages for mapping resistances. The genetic diversity of multiple parents, which has been recombined over several generations, leads to a broad phenotypic diversity, suitable for high-resolution mapping of quantitative traits. In this study, interval mapping was performed to map quantitative trait loci (QTL) for leaf rust resistance in the Bavarian MAGIC Wheat population, comprising 394 F6:8 recombinant inbred lines (RILs). Phenotypic evaluation of the RILs for adult plant resistance was carried out in field trials at three locations and two years, as well as in a controlled-environment seedling inoculation test. In total, interval mapping revealed 19 QTL, which corresponded to 11 distinct chromosomal regions controlling leaf rust resistance. Six of these regions may represent putative new QTL. Due to the elite parental material, RILs identified to be resistant to leaf rust can be easily introduced in breeding programs.
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Affiliation(s)
- Sandra Rollar
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
| | - Manuel Geyer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Lorenz Hartl
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Volker Mohler
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
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17
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Dinkar V, Jha SK, Mallick N, Niranjana M, Agarwal P, Sharma JB, Vinod. Molecular mapping of a new recessive wheat leaf rust resistance gene originating from Triticum spelta. Sci Rep 2020; 10:22113. [PMID: 33335131 PMCID: PMC7746701 DOI: 10.1038/s41598-020-78679-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/27/2020] [Indexed: 11/09/2022] Open
Abstract
TSD276-2, a wheat genetic stock derived from the cross Agra Local/T. spelta 276 showed broad spectrum resistance against leaf rust pathogen. Genetic analysis was undertaken using F1, F2, F2:3 and BC1F1 generations derived from the cross TSD276-2/Agra Local. The results revealed a single recessive gene for leaf rust resistance, tentatively named as LrTs276-2, in TSD276-2. Molecular mapping of leaf rust resistance gene LrTs276-2 in TSD276-2 was done using SNP-based PCR and SSR markers. For Bulked Segregant Analysis (BSA), two bulks viz. resistant bulk and susceptible bulk, and the parents TSD276-2 and Agra Local were genotyped for SNPs using AFFYMETRIX 35K Wheat Breeders' AXIOM array. T. spelta 276 was also genotyped and used as a check. BSA indicated that the gene for leaf rust resistance in TSD276-2 is located on chromosome arm 1DS. Putatively linked SNPs on chromosome arm 1DS were converted into PCR-based markers. Polymorphic SSR markers on chromosome arm 1DS were also identified. Final linkage map was constructed using one SNP-based PCR and three SSR markers. The rust reaction and chromosomal location suggest that LrTs276-2 is a new leaf rust resistance gene which may be useful in broadening the genetic base of leaf rust resistance in wheat.
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Affiliation(s)
- Vishal Dinkar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S K Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Niharika Mallick
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - M Niranjana
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Priyanka Agarwal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - J B Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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18
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Saripalli G, Singh K, Gautam T, Kumar S, Raghuvanshi S, Prasad P, Jain N, Sharma PK, Balyan HS, Gupta PK. Genome-wide analysis of H3K4me3 and H3K27me3 modifications due to Lr28 for leaf rust resistance in bread wheat (Triticum aestivum). PLANT MOLECULAR BIOLOGY 2020; 104:113-136. [PMID: 32627097 DOI: 10.1007/s11103-020-01029-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
Present study revealed a complex relationship among histone H3 methylation (examined using H3K4/K27me3 marks), cytosine DNA methylation and differential gene expression during Lr28 mediated leaf rust resistance in wheat. During the present study, genome-wide histone modifications were examined in a pair of near isogenic lines (NILs) (with and without Lr28 in the background of cv. HD2329). The two histone marks used included H3K4me3 (an activation mark) and H3K27me3 (a repression mark). The results were compared with levels of expression (using RNA-seq) and DNA methylation (MeDIP) data obtained using the same pair of NILs. Some of the salient features of the present study include the following: (i) large scale differential binding sites (DBS) were available for only H3K4me3 in the susceptible cultivar, but for both H3K4me3 and H3K27me3 in its resistant NIL; (ii) DBSs for H3K27me3 mark were more abundant (> 80%) in intergenic regions, whereas DBSs for H3K4me3 were distributed in all genomic regions including exons, introns, intergenic, TTS (transcription termination sites) and promoters; (iii) fourteen (14) genes associated with DBSs showed co-localization for both the marks; (iv) only a small fraction (7% for H3K4me3 and 12% for H3K27me3) of genes associated with DBSs matched with the levels of gene expression inferred from RNA-seq data; (v) validation studies using qRT-PCR were conducted on 26 selected representative genes; results for only 11 genes could be validated. The proteins encoded by important genes involved in promoting infection included domains generally carried by R gene proteins such as Mlo like protein, protein kinases and purple acid phosphatase. Similarly, proteins encoded by genes involved in resistance included those carrying domains for lectin kinase, R gene, aspartyl protease, etc. Overall, the results suggest a very complex network of downstream genes that are expressed during compatible and incompatible interactions; some of the genes identified during the present study may be used in future validation studies involving RNAi/overexpression approaches.
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Affiliation(s)
- Gautam Saripalli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India
| | - Kalpana Singh
- Bioinformatics Infrastructure Facility, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - Tinku Gautam
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India
| | - Santosh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Pramod Prasad
- Regional Station, Indian Institute of Wheat and Barley Research (IIWBR), Flowerdale, Shimla, HP, 171002, India
| | - Neelu Jain
- Division of Genetics and Plant Breeding, ICAR-IARI, Pusa, New Delhi, 110012, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India
- Bioinformatics Infrastructure Facility, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India.
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19
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Kumar D, Kumar A, Chhokar V, Gangwar OP, Bhardwaj SC, Sivasamy M, Prasad SVS, Prakasha TL, Khan H, Singh R, Sharma P, Sheoran S, Iquebal MA, Jaiswal S, Angadi UB, Singh G, Rai A, Singh GP, Kumar D, Tiwari R. Genome-Wide Association Studies in Diverse Spring Wheat Panel for Stripe, Stem, and Leaf Rust Resistance. FRONTIERS IN PLANT SCIENCE 2020; 11:748. [PMID: 32582265 PMCID: PMC7286347 DOI: 10.3389/fpls.2020.00748] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/12/2020] [Indexed: 05/20/2023]
Abstract
Among several important wheat foliar diseases, Stripe rust (YR), Leaf rust (LR), and Stem rust (SR) have always been an issue of concern to the farmers and wheat breeders. Evolution of virulent pathotypes of these rusts has posed frequent threats to an epidemic. Pyramiding rust-resistant genes are the most economical and environment-friendly approach in postponing this inevitable threat. To achieve durable long term resistance against the three rusts, an attempt in this study was made searching for novel sources of resistant alleles in a panel of 483 spring wheat genotypes. This is a unique and comprehensive study where evaluation of a diverse panel comprising wheat germplasm from various categories and adapted to different wheat agro-climatic zones was challenged with 18 pathotypes of the three rusts with simultaneous screening in field conditions. The panel was genotyped using 35K SNP array and evaluated for each rust at two locations for two consecutive crop seasons. High heritability estimates of disease response were observed between environments for each rust type. A significant effect of population structure in the panel was visible in the disease response. Using a compressed mixed linear model approach, 25 genomic regions were found associated with resistance for at least two rusts. Out of these, seven were associated with all the three rusts on chromosome groups 1 and 6 along with 2B. For resistance against YR, LR, and SR, there were 16, 18, and 27 QTL (quantitative trait loci) identified respectively, associated at least in two out of four environments. Several of these regions got annotated with resistance associated genes viz. NB-LRR, E3-ubiquitin protein ligase, ABC transporter protein, etc. Alien introgressed (on 1B and 3D) and pleiotropic (on 7D) resistance genes were captured in seedling and adult plant disease responses, respectively. The present study demonstrates the use of genome-wide association for identification of a large number of favorable alleles for leaf, stripe, and stem rust resistance for broadening the genetic base. Quick conversion of these QTL into user-friendly markers will accelerate the deployment of these resistance loci in wheat breeding programs.
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Affiliation(s)
- Deepender Kumar
- Department of Bio and Nanotechnology, Guru Jambheshwar University of Science and Technology, Hisar, India
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Animesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Vinod Chhokar
- Department of Bio and Nanotechnology, Guru Jambheshwar University of Science and Technology, Hisar, India
| | - Om Prakash Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | | | - M. Sivasamy
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, India
| | - S. V. Sai Prasad
- ICAR-Indian Agricultural Research Institute, Regional Station, Indore, India
| | - T. L. Prakasha
- ICAR-Indian Agricultural Research Institute, Regional Station, Indore, India
| | - Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Rajender Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Mir Asif Iquebal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ulavappa B. Angadi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Dinesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
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20
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Sidhu JS, Singh D, Gill HS, Brar NK, Qiu Y, Halder J, Al Tameemi R, Turnipseed B, Sehgal SK. Genome-Wide Association Study Uncovers Novel Genomic Regions Associated With Coleoptile Length in Hard Winter Wheat. Front Genet 2020; 10:1345. [PMID: 32117410 PMCID: PMC7025573 DOI: 10.3389/fgene.2019.01345] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/09/2019] [Indexed: 01/13/2023] Open
Abstract
Successful seedling establishment depends on the optimum depth of seed placement especially in drought-prone conditions, providing an opportunity to exploit subsoil water and increase winter survival in winter wheat. Coleoptile length is a key determinant for the appropriate depth at which seed can be sown. Thus, understanding the genetic basis of coleoptile length is necessary and important for wheat breeding. We conducted a genome-wide association study (GWAS) using a diverse panel of 298 winter wheat genotypes to dissect the genetic architecture of coleoptile length. We identified nine genomic regions associated with the coleoptile length on seven different chromosomes. Of the nine genomic regions, five have been previously reported in various studies, including one mapped to previously known Rht-B1 region. Three novel quantitative trait loci (QTLs), QCL.sdsu-2AS, QCL.sdsu-4BL, and QCL.sdsu-5BL were identified in our study. QCL.sdsu-5BL has a large substitution effect which is comparable to Rht-B1's effect and could be used to compensate for the negative effect of Rht-B1 on coleoptile length. In total, the nine QTLs explained 59% of the total phenotypic variation. Cultivars 'Agate' and 'MT06103' have the longest coleoptile length and interestingly, have favorable alleles at nine and eight coleoptile loci, respectively. These lines could be a valuable germplasm for longer coleoptile breeding. Gene annotations in the candidate regions revealed several putative proteins of specific interest including cytochrome P450-like, expansins, and phytochrome A. The QTLs for coleoptile length linked to single-nucleotide polymorphism (SNP) markers reported in this study could be employed in marker-assisted breeding for longer coleoptile in wheat. Thus, our study provides valuable insights into the genetic and molecular regulation of the coleoptile length in winter wheat.
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Affiliation(s)
- Jagdeep Singh Sidhu
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | - Dilkaran Singh
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
| | - Harsimardeep Singh Gill
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | - Navreet Kaur Brar
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | - Yeyan Qiu
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | - Jyotirmoy Halder
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | - Rami Al Tameemi
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | - Brent Turnipseed
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | - Sunish Kumar Sehgal
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
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Editorial for Special Issue "Molecular Advances in Wheat and Barley". Int J Mol Sci 2019; 20:ijms20143501. [PMID: 31315309 PMCID: PMC6678518 DOI: 10.3390/ijms20143501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 07/15/2019] [Accepted: 07/15/2019] [Indexed: 12/02/2022] Open
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