1
|
Li L, Yang J, Zhang Q, Xue Q, Li M, Xue Q, Liu W, Niu Z, Ding X. Genome-wide identification of Ankyrin (ANK) repeat gene families in three Dendrobium species and the expression of ANK genes in D. officinale under gibberellin and abscisic acid treatments. BMC PLANT BIOLOGY 2024; 24:762. [PMID: 39123107 PMCID: PMC11316315 DOI: 10.1186/s12870-024-05461-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Dendrobium Sw. represents one of the most expansive genera within the Orchidaceae family, renowned for its species' high medicinal and ornamental value. In higher plants, the ankyrin (ANK) repeat protein family is characterized by a unique ANK repeat domain, integral to a plethora of biological functions and biochemical activities. The ANK gene family plays a pivotal role in various plant physiological processes, including stress responses, hormone signaling, and growth. Hence, investigating the ANK gene family and identifying disease-resistance genes in Dendrobium is of paramount importance. RESULTS This research identified 78 ANK genes in Dendrobium officinale Kimura et Migo, 77 in Dendrobium nobile Lindl., and 58 in Dendrobium chrysotoxum Lindl. Subsequently, we conducted comprehensive bioinformatics analyses on these ANK gene families, encompassing gene classification, chromosomal localization, phylogenetic relationships, gene structure and motif characterization, cis-acting regulatory element identification, collinearity assessment, protein-protein interaction network construction, and gene expression profiling. Concurrently, three DoANK genes (DoANK14, DoANK19, and DoANK47) in D. officinale were discerned to indirectly activate the NPR1 transcription factor in the ETI system via SA, thereby modulating the expression of the antibacterial PR gene. Hormonal treatments with GA3 and ABA revealed that 17 and 8 genes were significantly up-regulated, while 4 and 8 genes were significantly down-regulated, respectively. DoANK32 was found to localize to the ArfGAP gene in the endocytosis pathway, impacting vesicle transport and the polar movement of auxin. CONCLUSION Our findings provide a robust framework for the taxonomic classification, evolutionary analysis, and functional prediction of Dendrobium ANK genes. The three highlighted ANK genes (DoANK14, DoANK19, and DoANK47) from D. officinale may prove valuable in disease resistance and stress response research. DoANK32 is implicated in the morphogenesis and development of D. officinale through its role in vesicular transport and auxin polarity, with subcellular localization studies confirming its presence in the nucleus and cell membrane. ANK genes displaying significant expression changes in response to hormonal treatments could play a crucial role in the hormonal response of D. officinale, potentially inhibiting its growth and development through the modulation of plant hormones such as GA3 and ABA.
Collapse
Affiliation(s)
- Lingli Li
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Jiapeng Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Qian Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Qiqian Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Meiqian Li
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China.
| |
Collapse
|
2
|
Yang J, Xiong C, Li S, Zhou C, Li L, Xue Q, Liu W, Niu Z, Ding X. Evolution patterns of NBS genes in the genus Dendrobium and NBS-LRR gene expression in D. officinale by salicylic acid treatment. BMC PLANT BIOLOGY 2022; 22:529. [PMID: 36376794 PMCID: PMC9661794 DOI: 10.1186/s12870-022-03904-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Dendrobium officinale Kimura et Migo, which contains rich polysaccharides, flavonoids and alkaloids, is a Traditional Chinese Medicine (TCM) with important economic benefits, while various pathogens have brought huge losses to its industrialization. NBS gene family is the largest class of plant disease resistance (R) genes, proteins of which are widely distributed in the upstream and downstream of the plant immune systems and are responsible for receiving infection signals and regulating gene expression respectively. It is of great significance for the subsequent disease resistance breeding of D. officinale to identify NBS genes by using the newly published high-quality chromosome-level D. officinale genome. RESULTS In this study, a total of 655 NBS genes were uncovered from the genomes of D. officinale, D. nobile, D. chrysotoxum, V. planifolia, A. shenzhenica, P. equestris and A. thaliana. The phylogenetic results of CNL-type protein sequences showed that orchid NBS-LRR genes have significantly degenerated on branches a and b. The Dendrobium NBS gene homology analysis showed that the Dendrobium NBS genes have two obvious characteristics: type changing and NB-ARC domain degeneration. Because the NBS-LRR genes have both NB-ARC and LRR domains, 22 D. officinale NBS-LRR genes were used for subsequent analyses, such as gene structures, conserved motifs, cis-elements and functional annotation analyses. All these results suggested that D. officinale NBS-LRR genes take part in the ETI system, plant hormone signal transduction pathway and Ras signaling pathway. Finally, there were 1,677 DEGs identified from the salicylic acid (SA) treatment transcriptome data of D. officinale. Among them, six NBS-LRR genes (Dof013264, Dof020566, Dof019188, Dof019191, Dof020138 and Dof020707) were significantly up-regulated. However, only Dof020138 was closely related to other pathways from the results of WGCNA, such as pathogen identification pathways, MAPK signaling pathways, plant hormone signal transduction pathways, biosynthetic pathways and energy metabolism pathways. CONCLUSION Our results revealed that the NBS gene degenerations are common in the genus Dendrobium, which is the main reason for the diversity of NBS genes, and the NBS-LRR genes generally take part in D. officinale ETI system and signal transduction pathways. In addition, the D. officinale NBS-LRR gene Dof020138, which may have an important breeding value, is indirectly activated by SA in the ETI system.
Collapse
Affiliation(s)
- Jiapeng Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Caijun Xiong
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Siyuan Li
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Cheng Zhou
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Lingli Li
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China.
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China.
| |
Collapse
|
3
|
Jin P, Chao K, Li J, Wang Z, Cheng P, Li Q, Wang B. Functional Verification of Two Genes Related to Stripe Rust Resistance in the Wheat- Leymus mollis Introgression Line M8664-3. FRONTIERS IN PLANT SCIENCE 2021; 12:754823. [PMID: 34759947 PMCID: PMC8574815 DOI: 10.3389/fpls.2021.754823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most widespread and destructive fungal diseases of wheat worldwide. The cultivation and growth of resistant wheat varieties are the most economical, effective, and environmental friendly methods to control stripe rust. Therefore, it is necessary to use new resistance genes to breed resistant wheat varieties. A single dominant gene temporarily designated as YrM8664-3, from a wheat-Leymus mollis introgression line M8664-3 highly resistant to Chinese predominant Pst races, is a potentially valuable source of stripe rust resistance for breeding. Herein, based on previous YrM8664-3 chromosome location results (bin 4AL13-0.59-0.66 close to 4AL12-0.43-0.59) and expression change information of candidate genes and bioinformatics analysis, several candidate genes with significantly different expression changes were then selected and verified by virus-induced gene silencing (VIGS). Two of the candidate genes temporarily designated as TaFBN [containing plastid lipid-associated proteins (PAP)_fibrillin domain in its protein] and Ta_Pes_BRCT [containing Pescadillo and breast cancer tumour suppressor protein C-terminus (BRCT) domain in its protein], produced the most significant resistance changes in the wheat-Pst interaction system after silencing. These two genes were further verified by Agrobacterium-mediated wheat genetic transformation technology. According to the identification of disease resistance, the resistance function of the candidate gene TaFBN was further verified. Then, the expression of TaFBN under hormone treatment indicated that TaFBN may be related to the salicylic acid (SA) and abscisic acid (ABA) signaling pathways. Combined with the expression of TaFBN in response to environmental stress stimulation, it can be reasonably speculated that TaFBN plays an important role in the resistance of wheat to Pst and is involved in abiotic stress pathways.
Collapse
Affiliation(s)
- Pengfei Jin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Kaixiang Chao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
- College of Chemistry, Biology and Environment, Yuxi Normal University, Yuxi, China
| | - Juan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
- Dingxi Plant Protection and Quarantine Station, Dingxi, China
| | - Zihao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Peng Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Qiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Baotong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| |
Collapse
|
4
|
Dong L, Huo N, Wang Y, Deal K, Wang D, Hu T, Dvorak J, Anderson OD, Luo MC, Gu YQ. Rapid evolutionary dynamics in a 2.8-Mb chromosomal region containing multiple prolamin and resistance gene families in Aegilops tauschii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:495-506. [PMID: 27228577 DOI: 10.1111/tpj.13214] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/03/2016] [Accepted: 05/09/2016] [Indexed: 06/05/2023]
Abstract
Prolamin and resistance gene families are important in wheat food use and in defense against pathogen attacks, respectively. To better understand the evolution of these multi-gene families, the DNA sequence of a 2.8-Mb genomic region, representing an 8.8 cM genetic interval and harboring multiple prolamin and resistance-like gene families, was analyzed in the diploid grass Aegilops tauschii, the D-genome donor of bread wheat. Comparison with orthologous regions from rice, Brachypodium, and sorghum showed that the Ae. tauschii region has undergone dramatic changes; it has acquired more than 80 non-syntenic genes and only 13 ancestral genes are shared among these grass species. These non-syntenic genes, including prolamin and resistance-like genes, originated from various genomic regions and likely moved to their present locations via sequence evolution processes involving gene duplication and translocation. Local duplication of non-syntenic genes contributed significantly to the expansion of gene families. Our analysis indicates that the insertion of prolamin-related genes occurred prior to the separation of the Brachypodieae and Triticeae lineages. Unlike in Brachypodium, inserted prolamin genes have rapidly evolved and expanded to encode different classes of major seed storage proteins in Triticeae species. Phylogenetic analyses also showed that the multiple insertions of resistance-like genes and subsequent differential expansion of each R gene family. The high frequency of non-syntenic genes and rapid local gene evolution correlate with the high recombination rate in the 2.8-Mb region with nine-fold higher than the genome-wide average. Our results demonstrate complex evolutionary dynamics in this agronomically important region of Triticeae species.
Collapse
Affiliation(s)
- Lingli Dong
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Naxin Huo
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yi Wang
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Karin Deal
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Daowen Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Tiezhu Hu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Olin D Anderson
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Yong Q Gu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA.
| |
Collapse
|
5
|
Liu F, Si H, Wang C, Sun G, Zhou E, Chen C, Ma C. Molecular evolution of Wcor15 gene enhanced our understanding of the origin of A, B and D genomes in Triticum aestivum. Sci Rep 2016; 6:31706. [PMID: 27526862 PMCID: PMC4985644 DOI: 10.1038/srep31706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/25/2016] [Indexed: 11/29/2022] Open
Abstract
The allohexaploid bread wheat originally derived from three closely related species with A, B and D genome. Although numerous studies were performed to elucidate its origin and phylogeny, no consensus conclusion has reached. In this study, we cloned and sequenced the genes Wcor15-2A, Wcor15-2B and Wcor15-2D in 23 diploid, 10 tetraploid and 106 hexaploid wheat varieties and analyzed their molecular evolution to reveal the origin of the A, B and D genome in Triticum aestivum. Comparative analyses of sequences in diploid, tetraploid and hexaploid wheats suggest that T. urartu, Ae. speltoides and Ae. tauschii subsp. strangulata are most likely the donors of the Wcor15-2A, Wcor15-2B and Wcor15-2D locus in common wheat, respectively. The Wcor15 genes from subgenomes A and D were very conservative without insertion and deletion of bases during evolution of diploid, tetraploid and hexaploid. Non-coding region of Wcor15-2B gene from B genome might mutate during the first polyploidization from Ae. speltoides to tetraploid wheat, however, no change has occurred for this gene during the second allopolyploidization from tetraploid to hexaploid. Comparison of the Wcor15 gene shed light on understanding of the origin of the A, B and D genome of common wheat.
Collapse
Affiliation(s)
- Fangfang Liu
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.,Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow &Huai River Valley, Ministry of Agriculture, Hefei 230036, China
| | - Hongqi Si
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.,Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow &Huai River Valley, Ministry of Agriculture, Hefei 230036, China
| | - Chengcheng Wang
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.,Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow &Huai River Valley, Ministry of Agriculture, Hefei 230036, China
| | - Genlou Sun
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.,Biology Department, Saint Mary's University, Halifax, NS, B3H 3C3 Canada
| | - Erting Zhou
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Can Chen
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Chuanxi Ma
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.,Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow &Huai River Valley, Ministry of Agriculture, Hefei 230036, China.,National United Engineering Laboratory for Crop Stress Resistance Breeding, Hefei 230036, China.,Anhui Key Laboratory of Crop Biology, Hefei 230036, China
| |
Collapse
|
6
|
Dramatic Number Variation of R Genes in Solanaceae Species Accounted for by a Few R Gene Subfamilies. PLoS One 2016; 11:e0148708. [PMID: 26849045 PMCID: PMC4743996 DOI: 10.1371/journal.pone.0148708] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/20/2016] [Indexed: 11/30/2022] Open
Abstract
Most disease resistance genes encode nucleotide-binding-site (NBS) and leucine-rich-repeat (LRR) domains, and the NBS-LRR encoding genes are often referred to as R genes. Using newly developed approach, 478, 485, 1,194, 1,665, 2,042 and 374 R genes were identified from the genomes of tomato Heinz1706, wild tomato LA716, potato DM1-3, pepper Zunla-1 and wild pepper Chiltepin and tobacco TN90, respectively. The majority of R genes from Solanaceae were grouped into 87 subfamilies, including 16 TIR-NBS-LRR (TNL) and 71 non-TNL subfamilies. Each subfamily was annotated manually, including identification of intron/exon structure and intron phase. Interestingly, TNL subfamilies have similar intron phase patterns, while the non-TNL subfamilies have diverse intron phase due to frequent gain of introns. Prevalent presence/absence polymorphic R gene loci were found among Solanaceae species, and an integrated map with 427 R loci was constructed. The pepper genome (2,042 in Chiltepin) has at least four times of R genes as in tomato (478 in Heinz1706). The high number of R genes in pepper genome is due to the amplification of R genes in a few subfamilies, such as the Rpi-blb2 and BS2 subfamilies. The mechanism underlying the variation of R gene number among different plant genomes is discussed.
Collapse
|
7
|
Yuan X, Yan C, Wu Z, Ren F, Zhang H, Baker B, Chen J, Kuang H. Frequent Gain and Loss of Resistance against Tobacco Mosaic Virus in Nicotiana Species. MOLECULAR PLANT 2015; 8:1813-5. [PMID: 26363271 DOI: 10.1016/j.molp.2015.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 08/25/2015] [Accepted: 09/05/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Xinjie Yuan
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Chenghuan Yan
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Zhujun Wu
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Feihong Ren
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Hui Zhang
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Barbara Baker
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Plant Gene Expression Center, US Department of Agriculture-Agricultural Research Service, Albany, CA 94710, USA
| | - Jiongjiong Chen
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Hanhui Kuang
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| |
Collapse
|
8
|
Identification of Immune Related LRR-Containing Genes in Maize (Zea mays L.) by Genome-Wide Sequence Analysis. Int J Genomics 2015; 2015:231358. [PMID: 26609518 PMCID: PMC4645488 DOI: 10.1155/2015/231358] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 09/27/2015] [Indexed: 11/25/2022] Open
Abstract
A large number of immune receptors consist of nucleotide binding site-leucine rich repeat (NBS-LRR) proteins and leucine rich repeat-receptor-like kinases (LRR-RLK) that play a crucial role in plant disease resistance. Although many NBS-LRR genes have been previously identified in Zea mays, there are no reports on identifying NBS-LRR genes encoded in the N-terminal Toll/interleukin-1 receptor (TIR) motif and identifying genome-wide LRR-RLK genes. In the present study, 151 NBS-LRR genes and 226 LRR-RLK genes were identified after performing bioinformatics analysis of the entire maize genome. Of these identified genes, 64 NBS-LRR genes and four TIR-NBS-LRR genes were identified for the first time. The NBS-LRR genes are unevenly distributed on each chromosome with gene clusters located at the distal end of each chromosome, while LRR-RLK genes have a random chromosomal distribution with more paired genes. Additionally, six LRR-RLK/RLPs including FLS2, PSY1R, PSKR1, BIR1, SERK3, and Cf5 were characterized in Zea mays for the first time. Their predicted amino acid sequences have similar protein structures with their respective homologues in other plants, indicating that these maize LRR-RLK/RLPs have the same functions as their homologues act as immune receptors. The identified gene sequences would assist in the study of their functions in maize.
Collapse
|
9
|
Urso S, Desiderio F, Biselli C, Bagnaresi P, Crispino L, Piffanelli P, Abbruscato P, Assenza F, Guarnieri G, Cattivelli L, Valè G. Genetic analysis of durable resistance to Magnaporthe oryzae in the rice accession Gigante Vercelli identified two blast resistance loci. Mol Genet Genomics 2015; 291:17-32. [PMID: 26141566 DOI: 10.1007/s00438-015-1085-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/24/2015] [Indexed: 12/21/2022]
Abstract
Rice cultivars exhibiting durable resistance to blast, the most important rice fungal disease provoking up to 30 % of rice losses, are very rare and searching for sources of such a resistance represents a priority for rice-breeding programs. To this aim we analyzed Gigante Vercelli (GV) and Vialone Nano (VN), two temperate japonica rice cultivars in Italy displaying contrasting response to blast, with GV showing a durable and broad-spectrum resistance, whereas VN being highly susceptible. An SSR-based genetic map developed using a GV × VN population segregating for blast resistance identified two blast resistance loci, localized to the long arm of chromosomes 1 and 4 explaining more than 78 % of the observed phenotypic variation for blast resistance. The pyramiding of two blast resistance QTLs was therefore involved in the observed durable resistance in GV. Mapping data were integrated with information obtained from RNA-seq expression profiling of all classes of resistance protein genes (resistance gene analogs, RGAs) and with the map position of known cloned or mapped blast resistance genes to search candidates for the GV resistant response. A co-localization of RGAs with the LOD peak or the marker interval of the chromosome 1 QTL was highlighted and a valuable tool for selecting the resistance gene during breeding programs was developed. Comparative analysis with known blast resistance genes revealed co-positional relationships between the chromosome 1 QTL with the Pi35/Pish blast resistance alleles and showed that the chromosome 4 QTL represents a newly identified blast resistance gene. The present genetic analysis has therefore allowed the identification of two blast resistance loci in the durable blast-resistant rice cultivar GV and tools for molecular selection of these resistance genes.
Collapse
Affiliation(s)
- Simona Urso
- Council for Agricultural Research and Economics (CRA), Genomics Research Centre, Via S. Protaso, 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics (CRA), Genomics Research Centre, Via S. Protaso, 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy
| | - Chiara Biselli
- Council for Agricultural Research and Economics (CRA), Genomics Research Centre, Via S. Protaso, 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy.,Council for Agricultural Research and Economics (CRA), Rice Research Unit, S.S. 11 to Torino, Km 2,5, 13100, Vercelli, Italy
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics (CRA), Genomics Research Centre, Via S. Protaso, 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy
| | - Laura Crispino
- Rice Genomics Group, Parco Tecnologico Padano, Via Einstein, 26900, Lodi, Italy
| | - Pietro Piffanelli
- Rice Genomics Group, Parco Tecnologico Padano, Via Einstein, 26900, Lodi, Italy
| | - Pamela Abbruscato
- Rice Genomics Group, Parco Tecnologico Padano, Via Einstein, 26900, Lodi, Italy
| | - Federica Assenza
- Council for Agricultural Research and Economics (CRA), Genomics Research Centre, Via S. Protaso, 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy.,Plant Biochemistry, Institute of Agricultural Sciences, ETH Zürich, LFW D 38 Universitätstrasse 2, 8092, Zurich, Switzerland
| | - Giada Guarnieri
- Council for Agricultural Research and Economics (CRA), Genomics Research Centre, Via S. Protaso, 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy.,Continental Semences S.p.A., via Monzato 9, 43029, Traversetolo, PR, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CRA), Genomics Research Centre, Via S. Protaso, 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy
| | - Giampiero Valè
- Council for Agricultural Research and Economics (CRA), Genomics Research Centre, Via S. Protaso, 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy. .,Council for Agricultural Research and Economics (CRA), Rice Research Unit, S.S. 11 to Torino, Km 2,5, 13100, Vercelli, Italy.
| |
Collapse
|
10
|
Jouet A, McMullan M, van Oosterhout C. The effects of recombination, mutation and selection on the evolution of the Rp1 resistance genes in grasses. Mol Ecol 2015; 24:3077-92. [PMID: 25907026 DOI: 10.1111/mec.13213] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 03/25/2015] [Accepted: 04/09/2015] [Indexed: 01/30/2023]
Abstract
Plant immune genes, or resistance genes, are involved in a co-evolutionary arms race with a diverse range of pathogens. In agronomically important grasses, such R genes have been extensively studied because of their role in pathogen resistance and in the breeding of resistant cultivars. In this study, we evaluate the importance of recombination, mutation and selection on the evolution of the R gene complex Rp1 of Sorghum, Triticum, Brachypodium, Oryza and Zea. Analyses show that recombination is widespread, and we detected 73 independent instances of sequence exchange, involving on average 1567 of 4692 nucleotides analysed (33.4%). We were able to date 24 interspecific recombination events and found that four occurred postspeciation, which suggests that genetic introgression took place between different grass species. Other interspecific events seemed to have been maintained over long evolutionary time, suggesting the presence of balancing selection. Significant positive selection (i.e. a relative excess of nonsynonymous substitutions (dN /dS >1)) was detected in 17-95 codons (0.42-2.02%). Recombination was significantly associated with areas with high levels of polymorphism but not with an elevated dN /dS ratio. Finally, phylogenetic analyses show that recombination results in a general overestimation of the divergence time (mean = 14.3%) and an alteration of the gene tree topology if the tree is not calibrated. Given that the statistical power to detect recombination is determined by the level of polymorphism of the amplicon as well as the number of sequences analysed, it is likely that many studies have underestimated the importance of recombination relative to the mutation rate.
Collapse
Affiliation(s)
- Agathe Jouet
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mark McMullan
- The Genome Analysis Center, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| |
Collapse
|
11
|
Ma J, Lei C, Xu X, Hao K, Wang J, Cheng Z, Ma X, Ma J, Zhou K, Zhang X, Guo X, Wu F, Lin Q, Wang C, Zhai H, Wang H, Wan J. Pi64, Encoding a Novel CC-NBS-LRR Protein, Confers Resistance to Leaf and Neck Blast in Rice. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:558-68. [PMID: 25650828 DOI: 10.1094/mpmi-11-14-0367-r] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Rice blast caused by Magnaporthe oryzae poses a major threat to rice production worldwide. The utilization of host resistance (R) genes is considered to be the most effective and economic means to control rice blast. Here, we show that the japonica landrace Yangmaogu (YMG) displays a broader spectrum of resistance to blast isolates than other previously reported broad-spectrum resistant (BSR) cultivars. Genetic analysis suggested that YMG contains at least three major R genes. One gene, Pi64, which exhibits resistance to indica-sourced isolate CH43 and several other isolates, was mapped to a 43-kb interval on chromosome 1 of YMG. Two open reading frames (NBS-1 and NBS-2) encoding nucleotide-binding site and leucine-rich repeat proteins were short-listed as candidate genes for Pi64. Constructs containing each candidate gene were transformed into three susceptible japonica cultivars. Only transformants with NBS-2 conferred resistance to leaf and neck blast, validating the idea that NBS-2 represents the functional Pi64 gene. Pi64 is constitutively expressed at all development stages and in all tissues examined. Pi64 protein is localized in both the cytoplasm and nucleus. Furthermore, introgression of Pi64 into susceptible cultivars via gene transformation and marker-assisted selection conferred high-level and broad-spectrum leaf and neck blast resistance to indica-sourced isolates, demonstrating its potential utility in breeding BSR rice cultivars.
Collapse
Affiliation(s)
- Jian Ma
- 1Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Cailin Lei
- 1Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Xingtao Xu
- 1Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Kun Hao
- 1Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Jiulin Wang
- 1Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Zhijun Cheng
- 1Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Xiaoding Ma
- 1Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Jin Ma
- 1Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Kunneng Zhou
- 2National Key Laboratory of Crop Genetics and Germplasm Enhancement / Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Zhang
- 1Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Xiuping Guo
- 1Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Fuqing Wu
- 1Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Qibing Lin
- 1Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Chunming Wang
- 2National Key Laboratory of Crop Genetics and Germplasm Enhancement / Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Nanjing 210095, China
| | - Huqu Zhai
- 1Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Haiyang Wang
- 1Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Jianmin Wan
- 1Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
- 2National Key Laboratory of Crop Genetics and Germplasm Enhancement / Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
12
|
Wei C, Kuang H, Li F, Chen J. The I2 resistance gene homologues in Solanum have complex evolutionary patterns and are targeted by miRNAs. BMC Genomics 2014; 15:743. [PMID: 25178990 PMCID: PMC4161772 DOI: 10.1186/1471-2164-15-743] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/26/2014] [Indexed: 11/10/2022] Open
Abstract
Background Several resistance traits, including the I2 resistance against tomato fusarium wilt, were mapped to the long arm of chromosome 11 of Solanum. However, the structure and evolution of this locus remain poorly understood. Results Comparative analysis showed that the structure and evolutionary patterns of the I2 locus vary considerably between potato and tomato. The I2 homologues from different Solanaceae species usually do not have orthologous relationship, due to duplication, deletion and frequent sequence exchanges. At least 154 sequence exchanges were detected among 76 tomato I2 homologues, but sequence exchanges between I2 homologues in potato is less frequent. Previous study showed that I2 homologues in potato were targeted by miR482. However, our data showed that I2 homologues in tomato were targeted by miR6024 rather than miR482. Furthermore, miR6024 triggers phasiRNAs from I2 homologues in tomato. Sequence analysis showed that miR6024 was originated after the divergence of Solanaceae. We hypothesized that miR6024 and miR482 might have facilitated the expansion of the I2 family in Solanaceae species, since they can minimize their potential toxic effects by down-regulating their expression. Conclusions The I2 locus represents a most divergent resistance gene cluster in Solanum. Its high divergence was partly due to frequent sequence exchanges between homologues. We propose that the successful expansion of I2 homologues in Solanum was at least partially attributed to miRNA mediated regulation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-743) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | - Jiongjiong Chen
- Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| |
Collapse
|
13
|
Abstract
This chapter describes a detailed protocol for genomic Southern blot analysis which can be used to detect transgene or endogenous gene sequences in cereal genomes. The protocol follows a standard approach that has been shown to generate high-quality results: size fractionation of genomic DNA; capillary transfer to a nylon membrane; hybridization with a digoxigenin-labelled probe; and detection using a chemiluminescent-based system. High sensitivity and limited background are key to successful Southern blots. The critical steps in this protocol are complete digestion of the right quantity of DNA, careful handling of the membrane to avoid unnecessary background, and optimization of probe concentration and temperatures during the hybridization step. Detailed instructions on how to successfully master these techniques are provided.
Collapse
Affiliation(s)
- Leigh Gebbie
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
14
|
Frequent loss of lineages and deficient duplications accounted for low copy number of disease resistance genes in Cucurbitaceae. BMC Genomics 2013; 14:335. [PMID: 23682795 PMCID: PMC3679737 DOI: 10.1186/1471-2164-14-335] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 05/14/2013] [Indexed: 11/25/2022] Open
Abstract
Background The sequenced genomes of cucumber, melon and watermelon have relatively few R-genes, with 70, 75 and 55 copies only, respectively. The mechanism for low copy number of R-genes in Cucurbitaceae genomes remains unknown. Results Manual annotation of R-genes in the sequenced genomes of Cucurbitaceae species showed that approximately half of them are pseudogenes. Comparative analysis of R-genes showed frequent loss of R-gene loci in different Cucurbitaceae species. Phylogenetic analysis, data mining and PCR cloning using degenerate primers indicated that Cucurbitaceae has limited number of R-gene lineages (subfamilies). Comparison between R-genes from Cucurbitaceae and those from poplar and soybean suggested frequent loss of R-gene lineages in Cucurbitaceae. Furthermore, the average number of R-genes per lineage in Cucurbitaceae species is approximately 1/3 that in soybean or poplar. Therefore, both loss of lineages and deficient duplications in extant lineages accounted for the low copy number of R-genes in Cucurbitaceae. No extensive chimeras of R-genes were found in any of the sequenced Cucurbitaceae genomes. Nevertheless, one lineage of R-genes from Trichosanthes kirilowii, a wild Cucurbitaceae species, exhibits chimeric structures caused by gene conversions, and may contain a large number of distinct R-genes in natural populations. Conclusions Cucurbitaceae species have limited number of R-gene lineages and each genome harbors relatively few R-genes. The scarcity of R-genes in Cucurbitaceae species was due to frequent loss of R-gene lineages and infrequent duplications in extant lineages. The evolutionary mechanisms for large variation of copy number of R-genes in different plant species were discussed.
Collapse
|
15
|
Joshi RK, Nayak S. Perspectives of genomic diversification and molecular recombination towards R-gene evolution in plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2013; 19:1-9. [PMID: 24381433 PMCID: PMC3550690 DOI: 10.1007/s12298-012-0138-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Plants are under strong evolutionary pressure in developing new and noble R genes to recognize pathogen avirulence (avr) determinants and bring about stable defense for generation after generations. Duplication, sequence variation by mutation, disparity in the length and structure of leucine rich repeats etc., causes tremendous variations within and among R genes in a plant thereby developing diverse recognitional specificity suitable enough for defense against new pathogens. Recent studies on genome sequencing, diversity and population genetics in different plants have thrown new insights on the molecular evolution of these genes. Tandem and segmental duplication are important factors in R gene abundance as inferred from the distribution of major nucleotide binding site-leucine rich repeats (NBS-LRRs) type R-genes in plant genomes. Likewise, R-gene evolution is also thought to be facilitated by cluster formation thereby causing recombination and sequence exchange and resulting in haplotypic diversity. Population studies have further proven that balancing selection is responsible for the maintenance of allelic diversity in R genes. In this review, we emphasize and discuss on improved perspectives towards the molecular mechanisms and selection pressure responsible for the evolution of NBS-LRR class resistance genes in plants.
Collapse
Affiliation(s)
- Raj Kumar Joshi
- Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, 751003 India
| | - Sanghamitra Nayak
- Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, 751003 India
| |
Collapse
|
16
|
Michelmore RW, Christopoulou M, Caldwell KS. Impacts of resistance gene genetics, function, and evolution on a durable future. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:291-319. [PMID: 23682913 DOI: 10.1146/annurev-phyto-082712-102334] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Studies on resistance gene function and evolution lie at the confluence of structural and molecular biology, genetics, and plant breeding. However, knowledge from these disparate fields has yet to be extensively integrated. This review draws on ideas and information from these different fields to elucidate the influences driving the evolution of different types of resistance genes in plants and the concurrent evolution of virulence in pathogens. It provides an overview of the factors shaping the evolution of recognition, signaling, and response genes in the context of emerging functional information along with a consideration of the new opportunities for durable resistance enabled by high-throughput DNA sequencing technologies.
Collapse
|
17
|
Luo S, Zhang Y, Hu Q, Chen J, Li K, Lu C, Liu H, Wang W, Kuang H. Dynamic nucleotide-binding site and leucine-rich repeat-encoding genes in the grass family. PLANT PHYSIOLOGY 2012; 159:197-210. [PMID: 22422941 PMCID: PMC3375961 DOI: 10.1104/pp.111.192062] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 03/12/2012] [Indexed: 05/20/2023]
Abstract
The proper use of resistance genes (R genes) requires a comprehensive understanding of their genomics and evolution. We analyzed genes encoding nucleotide-binding sites and leucine-rich repeats in the genomes of rice (Oryza sativa), maize (Zea mays), sorghum (Sorghum bicolor), and Brachypodium distachyon. Frequent deletions and translocations of R genes generated prevalent presence/absence polymorphism between different accessions/species. The deletions were caused by unequal crossover, homologous repair, nonhomologous repair, or other unknown mechanisms. R gene loci identified from different genomes were mapped onto the chromosomes of rice cv Nipponbare using comparative genomics, resulting in an integrated map of 495 R loci. Sequence analysis of R genes from the partially sequenced genomes of an African rice cultivar and 10 wild accessions suggested that there are many additional R gene lineages in the AA genome of Oryza. The R genes with chimeric structures (termed type I R genes) are diverse in different rice accessions but only account for 5.8% of all R genes in the Nipponbare genome. In contrast, the vast majority of R genes in the rice genome are type II R genes, which are highly conserved in different accessions. Surprisingly, pseudogene-causing mutations in some type II lineages are often conserved, indicating that their conservations were not due to their functions. Functional R genes cloned from rice so far have more type II R genes than type I R genes, but type I R genes are predicted to contribute considerable diversity in wild species. Type I R genes tend to reduce the microsynteny of their flanking regions significantly more than type II R genes, and their flanking regions have slightly but significantly lower G/C content than those of type II R genes.
Collapse
Affiliation(s)
| | | | - Qun Hu
- Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People’s Republic of China, 430070 (S.L., Y.Z., Q.H., J.C., K.L, C.L., H.K.); and Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People’s Republic of China, 650223 (H.L., W.W.)
| | - Jiongjiong Chen
- Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People’s Republic of China, 430070 (S.L., Y.Z., Q.H., J.C., K.L, C.L., H.K.); and Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People’s Republic of China, 650223 (H.L., W.W.)
| | - Kunpeng Li
- Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People’s Republic of China, 430070 (S.L., Y.Z., Q.H., J.C., K.L, C.L., H.K.); and Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People’s Republic of China, 650223 (H.L., W.W.)
| | - Chen Lu
- Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People’s Republic of China, 430070 (S.L., Y.Z., Q.H., J.C., K.L, C.L., H.K.); and Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People’s Republic of China, 650223 (H.L., W.W.)
| | - Hui Liu
- Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People’s Republic of China, 430070 (S.L., Y.Z., Q.H., J.C., K.L, C.L., H.K.); and Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People’s Republic of China, 650223 (H.L., W.W.)
| | - Wen Wang
- Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People’s Republic of China, 430070 (S.L., Y.Z., Q.H., J.C., K.L, C.L., H.K.); and Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People’s Republic of China, 650223 (H.L., W.W.)
| | - Hanhui Kuang
- Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People’s Republic of China, 430070 (S.L., Y.Z., Q.H., J.C., K.L, C.L., H.K.); and Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People’s Republic of China, 650223 (H.L., W.W.)
| |
Collapse
|
18
|
Barbieri M, Marcel TC, Niks RE, Francia E, Pasquariello M, Mazzamurro V, Garvin DF, Pecchioni N. QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L. Genome 2012; 55:152-63. [PMID: 22321152 DOI: 10.1139/g2012-001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The potential of the model grass Brachypodium distachyon L. (Brachypodium) for studying grass-pathogen interactions is still underexploited. We aimed to identify genomic regions in Brachypodium associated with quantitative resistance to the false brome rust fungus Puccinia brachypodii . The inbred lines Bd3-1 and Bd1-1, differing in their level of resistance to P. brachypodii, were crossed to develop an F(2) population. This was evaluated for reaction to a virulent isolate of P. brachypodii at both the seedling and advanced growth stages. To validate the results obtained on the F(2), resistance was quantified in F(2)-derived F(3) families in two experiments. Disease evaluations showed quantitative and transgressive segregation for resistance. A new AFLP-based Brachypodium linkage map consisting of 203 loci and spanning 812 cM was developed and anchored to the genome sequence with SSR and SNP markers. Three false brome rust resistance QTLs were identified on chromosomes 2, 3, and 4, and they were detected across experiments. This study is the first quantitative trait analysis in Brachypodium. Resistance to P. brachypodii was governed by a few QTLs: two acting at the seedling stage and one acting at both seedling and advanced growth stages. The results obtained offer perspectives to elucidate the molecular basis of quantitative resistance to rust fungi.
Collapse
Affiliation(s)
- Mirko Barbieri
- Dipartimento di Scienze Agrarie e degli Alimenti, Università di Modena e Reggio Emilia, Italy
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Fu YB. Population-based resequencing analysis of wild and cultivated barley revealed weak domestication signal of selection and bottleneck in the Rrs2 scald resistance gene region. Genome 2012; 55:93-104. [PMID: 22272833 DOI: 10.1139/g11-082] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Many plant disease resistance (R) genes have been cloned, but the potential of utilizing these plant R-gene genomic resources for genetic inferences of plant domestication history remains unexplored. A population-based resequencing analysis of the genomic region near the Rrs2 scald resistance gene was made in 51 accessions of wild and cultivated barley from 41 countries. Fifteen primer pairs were designed to sample the genomic region with a total length of 10 406 bp. More nucleotide diversity was found in wild (π = 0.01846) than cultivated (π = 0.01507) barley samples. Three distinct groups of 29 haplotypes were detected for all 51 samples, and they were well mixed with wild and cultivated barley samples from different countries and regions. The neutrality tests by Tajima's D were not significant, but a significant (P < 0.05) case by Fu and Li's D* and F* was found in the barley cultivar samples. The estimate of selection intensity by K(a)/K(s) was 0.691 in wild barley and 0.580 in cultivated barley. The estimate of the minimum recombination events was 16 in wild barley and 19 in cultivated barley. A coalescence simulation revealed a bottleneck intensity of 1.5 to 2 since barley domestication. Together, the domestication signal in the genomic region was weak both in human selection and domestication bottleneck.
Collapse
Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada.
| |
Collapse
|
20
|
Martin T, Biruma M, Fridborg I, Okori P, Dixelius C. A highly conserved NB-LRR encoding gene cluster effective against Setosphaeria turcica in sorghum. BMC PLANT BIOLOGY 2011; 11:151. [PMID: 22050783 PMCID: PMC3262770 DOI: 10.1186/1471-2229-11-151] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 11/03/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND The fungal pathogen Setosphaeria turcica causes turcicum or northern leaf blight disease on maize, sorghum and related grasses. A prevalent foliar disease found worldwide where the two host crops, maize and sorghum are grown. The aim of the present study was to find genes controlling the host defense response to this devastating plant pathogen. A cDNA-AFLP approach was taken to identify candidate sequences, which functions were further validated via virus induced gene silencing (VIGS), and real-time PCR analysis. Phylogenetic analysis was performed to address evolutionary events. RESULTS cDNA-AFLP analysis was run on susceptible and resistant sorghum and maize genotypes to identify resistance-related sequences. One CC-NB-LRR encoding gene GRMZM2G005347 was found among the up-regulated maize transcripts after fungal challenge. The new plant resistance gene was designated as St referring to S. turcica. Genome sequence comparison revealed that the CC-NB-LRR encoding St genes are located on chromosome 2 in maize, and on chromosome 5 in sorghum. The six St sorghum genes reside in three pairs in one locus. When the sorghum St genes were silenced via VIGS, the resistance was clearly compromised, an observation that was supported by real-time PCR. Database searches and phylogenetic analysis suggest that the St genes have a common ancestor present before the grass subfamily split 50-70 million years ago. Today, 6 genes are present in sorghum, 9 in rice and foxtail millet, respectively, 3 in maize and 4 in Brachypodium distachyon. The St gene homologs have all highly conserved sequences, and commonly reside as gene pairs in the grass genomes. CONCLUSIONS Resistance genes to S. turcica, with a CC-NB-LRR protein domain architecture, have been found in maize and sorghum. VIGS analysis revealed their importance in the surveillance to S. turcica in sorghum. The St genes are highly conserved in sorghum, rice, foxtail millet, maize and Brachypodium, suggesting an essential evolutionary function.
Collapse
Affiliation(s)
- Tom Martin
- SLU, Uppsala Biocenter, Dept. Plant Biology and Forest Genetics, Uppsala P.O. Box 7080, S-750 07, Uppsala, Sweden
| | - Moses Biruma
- Dept. of Crop Science, Makerere University P.O. Box 7062, Kampala, Uganda
- National Agriculture Research Organisation, P.O. Box 295, Entebbe, Uganda
| | - Ingela Fridborg
- SLU, Uppsala Biocenter, Dept. Plant Biology and Forest Genetics, Uppsala P.O. Box 7080, S-750 07, Uppsala, Sweden
| | - Patrick Okori
- Dept. of Crop Science, Makerere University P.O. Box 7062, Kampala, Uganda
| | - Christina Dixelius
- SLU, Uppsala Biocenter, Dept. Plant Biology and Forest Genetics, Uppsala P.O. Box 7080, S-750 07, Uppsala, Sweden
| |
Collapse
|
21
|
Wang J, Tan S, Zhang L, Li P, Tian D. Co-variation among major classes of LRR-encoding genes in two pairs of plant species. J Mol Evol 2011; 72:498-509. [PMID: 21626302 DOI: 10.1007/s00239-011-9448-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 05/10/2011] [Indexed: 10/18/2022]
Abstract
NBS-LRR (nucleotide-binding site-leucine-rich repeat), LRR-RLK (LRR-receptor-like kinase), and LRR-only are the three major LRR-encoding genes. Owing to the crucial role played by them in plant resistance, development, and growth, extensive studies have been performed on the NBS-LRR and LRR-RLK genes. However, few studies have focused on these genes collectively; they may co-vary as all of them contain LRR motifs. To investigate their common evolutionary patterns, all major classes of LRR-encoding genes were identified in 12 plant species, and particularly compared in two pairs of close relatives, Arabidopsis thaliana-A. lyrata (At-Al) and Zea mays-Sorghum bicolor. Our results showed that these genes co-vary significantly in terms of their numbers between species and that the genes with certain evolutionary parameters are most likely to have similar functions. The development-related genes have clear orthologous relationships between closely related species, as well as lower nucleotide divergence, and Ka/Ks ratio. In contrast, resistance-related genes have exactly opposite characteristics and favor 11-15 LRRs per gene. This association could be very useful in predicting the function of LRR-encoding genes. The presence of co-variation suggests that LRRs, combined with other domains, can work better in some common functions. In order to cooperate efficiently, there should be balanced gene numbers among the different gene classes.
Collapse
Affiliation(s)
- Jiao Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, China
| | | | | | | | | |
Collapse
|
22
|
Ribas AF, Cenci A, Combes MC, Etienne H, Lashermes P. Organization and molecular evolution of a disease-resistance gene cluster in coffee trees. BMC Genomics 2011; 12:240. [PMID: 21575174 PMCID: PMC3113787 DOI: 10.1186/1471-2164-12-240] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 05/16/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most disease-resistance (R) genes in plants encode NBS-LRR proteins and belong to one of the largest and most variable gene families among plant genomes. However, the specific evolutionary routes of NBS-LRR encoding genes remain elusive. Recently in coffee tree (Coffea arabica), a region spanning the SH3 locus that confers resistance to coffee leaf rust, one of the most serious coffee diseases, was identified and characterized. Using comparative sequence analysis, the purpose of the present study was to gain insight into the genomic organization and evolution of the SH3 locus. RESULTS Sequence analysis of the SH3 region in three coffee genomes, Ea and Ca subgenomes from the allotetraploid C. arabica and Cc genome from the diploid C. canephora, revealed the presence of 5, 3 and 4 R genes in Ea, Ca, and Cc genomes, respectively. All these R-gene sequences appeared to be members of a CC-NBS-LRR (CNL) gene family that was only found at the SH3 locus in C. arabica. Furthermore, while homologs were found in several dicot species, comparative genomic analysis failed to find any CNL R-gene in the orthologous regions of other eudicot species. The orthology relationship among the SH3-CNL copies in the three analyzed genomes was determined and the duplication/deletion events that shaped the SH3 locus were traced back. Gene conversion events were detected between paralogs in all three genomes and also between the two sub-genomes of C. arabica. Significant positive selection was detected in the solvent-exposed residues of the SH3-CNL copies. CONCLUSION The ancestral SH3-CNL copy was inserted in the SH3 locus after the divergence between Solanales and Rubiales lineages. Moreover, the origin of most of the SH3-CNL copies predates the divergence between Coffea species. The SH3-CNL family appeared to evolve following the birth-and-death model, since duplications and deletions were inferred in the evolution of the SH3 locus. Gene conversion between paralog members, inter-subgenome sequence exchanges and positive selection appear to be the major forces acting on the evolution of SH3-CNL in coffee trees.
Collapse
Affiliation(s)
- Alessandra F Ribas
- IRD - Institut de Recherche pour le Développement, UMR RPB, Montpellier Cedex, France
| | | | | | | | | |
Collapse
|