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Kaur B, Bai BK, Dhillon GS, Kaur J, Sharma A, Srivastava P, Chhuneja P, Kaur S. Mapping of Aegilops speltoides derived leaf rust and stripe rust resistance genes using 35K SNP array. BMC Genom Data 2024; 25:69. [PMID: 39009972 PMCID: PMC11247808 DOI: 10.1186/s12863-024-01247-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/19/2024] [Indexed: 07/17/2024] Open
Abstract
Wheat is an essential food commodity cultivated throughout the world. However, this crop faces continuous threats from fungal pathogens, leaf rust (LR) and stripe rust (YR). To continue feeding the growing population, these major destructors of wheat must be effectively countered by enhancing the genetic diversity of cultivated germplasm. In this study, an introgression line with hexaploid background (ILsp3603) carrying resistance against Pt pathotypes 77-5 (121R63-1), 77-9 (121R60-1) and Pst pathotypes 46S119 (46E159), 110S119 (110E159), 238S119 (238E159) was developed from donor wheat wild progenitor, Aegilops speltoides acc pau 3603. To understand the genetic basis of resistance and map these genes (named Lrsp3603 and Yrsp3603), inheritance studies were carried out in F6 and F7 mapping population, developed by crossing ILsp3603 with LR and YR susceptible cultivar WL711, which revealed a monogenic (single gene) inheritance pattern for each of these traits. Bulk segregant analysis combined with 35 K Axiom SNP array genotyping mapped both genes as separate entities on the short arm of chromosome 6B. A genetic linkage map, comprising five markers, 1 SNP, 1 PLUG and three gene based SSRs, covered a genetic distance of 12.65 cM. Lrsp3603 was flanked by markers Tag-SSR14 (located proximally at 2.42 cM) and SNP AX-94542331 (at 3.28 cM) while Yrsp3603 was mapped at one end closest to AX-94542331 at 6.62 cM distance. Functional annotation of Lrsp3603 target region (∼ 1 Mbp) revealed 10 gene IDs associated with disease resistance mechanisms including three encoding typical R gene domains.
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Affiliation(s)
- Balihar Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Bukke Kutti Bai
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | | | - Jaspal Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India
| | - Achla Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India.
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Xun H, Lv R, Yu Y, Yao J, Wang R, Sha Y, Wang H, Zhang D, Xu C, Wang T, Zhang Z, Liu B, Gong L. Evolutionary genomics of two diploid goat grass species belonging to the section Sitopsis of Aegilops, Aegilops longissima, and Aegilops sharonensis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38859560 DOI: 10.1111/tpj.16876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/12/2024]
Abstract
Aegilops longissima and Ae. sharonensis, being classified into the Sitopsis section of genus Aegilops, are distinct species both taxonomically and ecologically. Nevertheless, earlier observations indicate that the two species are not reproductively isolated to full extent and can inter-bred upon secondary contact. However, the genomic underpinnings of the morpho-ecological differentiation between the two foci species remained unexplored. Here, we resequenced 31 representative accessions of the two species and conducted in-depth comparative genomic analyses. We demonstrate recurrent and ongoing natural hybridizations between Ae. longissima and Ae. sharonensis, and depict features of genome composition of the resultant hybrids at both individual and population levels. We also delineate genomic regions and candidate genes potentially underpinning the differential morphological and edaphic adaptations of the two species. Intriguingly, a binary morphology was observed in the hybrids, suggesting existence of highly diverged genomic regions that remain uneroded by the admixtures. Together, our results provide new insights into the molding effects of interspecific hybridization on genome composition and mechanisms preventing merge of the two species.
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Affiliation(s)
- Hongwei Xun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yue Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jinyang Yao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ruisi Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yan Sha
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Han Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Deshi Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Li Y, Li Y, Zou X, Jiang S, Cao M, Chen F, Yin Y, Xiao W, Liu S, Guo X. Bioinformatic Identification and Expression Analyses of the MAPK-MAP4K Gene Family Reveal a Putative Functional MAP4K10-MAP3K7/8-MAP2K1/11-MAPK3/6 Cascade in Wheat ( Triticum aestivum L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:941. [PMID: 38611471 PMCID: PMC11013086 DOI: 10.3390/plants13070941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
The mitogen-activated protein kinase (MAPK) cascades act as crucial signaling modules that regulate plant growth and development, response to biotic/abiotic stresses, and plant immunity. MAP3Ks can be activated through MAP4K phosphorylation in non-plant systems, but this has not been reported in plants to date. Here, we identified a total of 234 putative TaMAPK family members in wheat (Triticum aestivum L.). They included 48 MAPKs, 17 MAP2Ks, 144 MAP3Ks, and 25 MAP4Ks. We conducted systematic analyses of the evolution, domain conservation, interaction networks, and expression profiles of these TaMAPK-TaMAP4K (representing TaMAPK, TaMAP2K, TaMAP3K, and TaMAP4K) kinase family members. The 234 TaMAPK-TaMAP4Ks are distributed on 21 chromosomes and one unknown linkage group (Un). Notably, 25 of these TaMAP4K family members possessed the conserved motifs of MAP4K genes, including glycine-rich motif, invariant lysine (K) motif, HRD motif, DFG motif, and signature motif. TaMAPK3 and 6, and TaMAP4K10/24 were shown to be strongly expressed not only throughout the growth and development stages but also in response to drought or heat stress. The bioinformatics analyses and qRT-PCR results suggested that wheat may activate the MAP4K10-MEKK7-MAP2K11-MAPK6 pathway to increase drought resistance in wheat, and the MAP4K10-MAP3K8-MAP2K1/11-MAPK3 pathway may be involved in plant growth. In general, our work identified members of the MAPK-MAP4K cascade in wheat and profiled their potential roles during their response to abiotic stresses and plant growth based on their expression pattern. The characterized cascades might be good candidates for future crop improvement and molecular breeding.
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Affiliation(s)
- Yongliang Li
- College of Biology, Hunan University, Changsha 410082, China
- Chongqing Research Institute, Hunan University, Chongqing 401120, China; (Y.L.); (Y.L.); (X.Z.); (S.J.); (M.C.); (F.C.); (Y.Y.)
| | - You Li
- College of Biology, Hunan University, Changsha 410082, China
| | - Xiaoxiao Zou
- College of Biology, Hunan University, Changsha 410082, China
| | - Shuai Jiang
- College of Biology, Hunan University, Changsha 410082, China
| | - Miyuan Cao
- College of Biology, Hunan University, Changsha 410082, China
| | - Fenglin Chen
- College of Biology, Hunan University, Changsha 410082, China
| | - Yan Yin
- College of Biology, Hunan University, Changsha 410082, China
| | - Wenjun Xiao
- College of Biology, Hunan University, Changsha 410082, China
- Chongqing Research Institute, Hunan University, Chongqing 401120, China; (Y.L.); (Y.L.); (X.Z.); (S.J.); (M.C.); (F.C.); (Y.Y.)
| | - Shucan Liu
- College of Biology, Hunan University, Changsha 410082, China
- Chongqing Research Institute, Hunan University, Chongqing 401120, China; (Y.L.); (Y.L.); (X.Z.); (S.J.); (M.C.); (F.C.); (Y.Y.)
| | - Xinhong Guo
- College of Biology, Hunan University, Changsha 410082, China
- Chongqing Research Institute, Hunan University, Chongqing 401120, China; (Y.L.); (Y.L.); (X.Z.); (S.J.); (M.C.); (F.C.); (Y.Y.)
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Bazile J, Nadaud I, Lasserre-Zuber P, Kitt J, De Oliveira R, Choulet F, Sourdille P. TaRECQ4 contributes to maintain both homologous and homoeologous recombination during wheat meiosis. FRONTIERS IN PLANT SCIENCE 2024; 14:1342976. [PMID: 38348162 PMCID: PMC10859459 DOI: 10.3389/fpls.2023.1342976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 12/29/2023] [Indexed: 02/15/2024]
Abstract
Introduction Meiotic recombination (or crossover, CO) is essential for gamete fertility as well as for alleles and genes reshuffling that is at the heart of plant breeding. However, CO remains a limited event, which strongly hampers the rapid production of original and improved cultivars. RecQ4 is a gene encoding a helicase protein that, when mutated, contributes to improve recombination rate in all species where it has been evaluated so far. Methods In this study, we developed wheat (Triticum aestivum L.) triple mutant (TM) for the three homoeologous copies of TaRecQ4 as well as mutants for two copies and heterozygous for the last one (Htz-A, Htz-B, Htz-D). Results Phenotypic observation revealed a significant reduction of fertility and pollen viability in TM and Htz-B plants compared to wild type plants suggesting major defects during meiosis. Cytogenetic analyses of these plants showed that complete absence of TaRecQ4 as observed in TM plants, leads to chromosome fragmentation during the pachytene stage, resulting in problems in the segregation of chromosomes during meiosis. Htz-A and Htz-D mutants had an almost normal meiotic progression indicating that both TaRecQ4-A and TaRecQ4-D copies are functional and that there is no dosage effect for TaRecQ4 in bread wheat. On the contrary, the TaRecQ4-B copy seems knocked-out, probably because of a SNP leading to a Threonine>Alanine change at position 539 (T539A) of the protein, that occurs in the crucial helicase ATP bind/DEAD/ResIII domain which unwinds nucleic acids. Occurrence of numerous multivalents in TM plants suggests that TaRecQ4 could also play a role in the control of homoeologous recombination. Discussion These findings provide a foundation for further molecular investigations into wheat meiosis regulation to fully understand the underlying mechanisms of how TaRecQ4 affects chiasma formation, as well as to identify ways to mitigate these defects and enhance both homologous and homoeologous recombination efficiency in wheat.
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Affiliation(s)
- Jeanne Bazile
- INRAE, UMR 1095 INRAE – UCA Genetics, Diversity & Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Isabelle Nadaud
- INRAE, UMR 1095 INRAE – UCA Genetics, Diversity & Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Pauline Lasserre-Zuber
- INRAE, UMR 1095 INRAE – UCA Genetics, Diversity & Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Jonathan Kitt
- INRAE, UMR 1095 INRAE – UCA Genetics, Diversity & Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Romain De Oliveira
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frédéric Choulet
- INRAE, UMR 1095 INRAE – UCA Genetics, Diversity & Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Pierre Sourdille
- INRAE, UMR 1095 INRAE – UCA Genetics, Diversity & Ecophysiology of Cereals, Clermont-Ferrand, France
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Cui L, Cheng H, Yang Z, Xia C, Zhang L, Kong X. Comparative Analysis Reveals Different Evolutionary Fates and Biological Functions in Wheat Duplicated Genes ( Triticum aestivum L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:3021. [PMID: 37687268 PMCID: PMC10489728 DOI: 10.3390/plants12173021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
Wheat (Triticum aestivum L.) is a staple food crop that provides 20% of total human calorie consumption. Gene duplication has been considered to play an important role in evolution by providing new genetic resources. However, the evolutionary fates and biological functions of the duplicated genes in wheat remain to be elucidated. In this study, the resulting data showed that the duplicated genes evolved faster with shorter gene lengths, higher codon usage bias, lower expression levels, and higher tissue specificity when compared to non-duplicated genes. Our analysis further revealed functions of duplicated genes in various biological processes with significant enrichment to environmental stresses. In addition, duplicated genes derived from dispersed, proximal, tandem, transposed, and whole-genome duplication differed in abundance, evolutionary rate, gene compactness, expression pattern, and genetic diversity. Tandem and proximal duplicates experienced stronger selective pressure and showed a more compact gene structure with diverse expression profiles than other duplication modes. Moreover, genes derived from different duplication modes showed an asymmetrical evolutionary pattern for wheat A, B, and D subgenomes. Several candidate duplication hotspots associated with wheat domestication or polyploidization were characterized as potential targets for wheat molecular breeding. Our comprehensive analysis revealed the evolutionary trajectory of duplicated genes and laid the foundation for future functional studies on wheat.
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Affiliation(s)
- Licao Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.C.); (H.C.); (Z.Y.); (C.X.); (L.Z.)
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Hao Cheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.C.); (H.C.); (Z.Y.); (C.X.); (L.Z.)
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Zhe Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.C.); (H.C.); (Z.Y.); (C.X.); (L.Z.)
| | - Chuan Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.C.); (H.C.); (Z.Y.); (C.X.); (L.Z.)
| | - Lichao Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.C.); (H.C.); (Z.Y.); (C.X.); (L.Z.)
| | - Xiuying Kong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.C.); (H.C.); (Z.Y.); (C.X.); (L.Z.)
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