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Chen X, Yao C, Liu J, Liu J, Fang J, Deng H, Yao Q, Kang T, Guo X. Basic helix-loop-helix (bHLH) gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses. BMC Genomics 2024; 25:67. [PMID: 38233751 PMCID: PMC10792839 DOI: 10.1186/s12864-023-09911-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Rye (Secale cereale), one of the drought and cold-tolerant crops, is an important component of the Triticae Dumortier family of Gramineae plants. Basic helix-loop-helix (bHLH), an important family of transcription factors, has played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. However, no systemic analysis of the bHLH transcription factor family has yet been reported in rye. RESULTS In this study, 220 bHLH genes in S. cereale (ScbHLHs) were identified and named based on the chromosomal location. The evolutionary relationships, classifications, gene structures, motif compositions, chromosome localization, and gene replication events in these ScbHLH genes are systematically analyzed. These 220 ScbHLH members are divided into 21 subfamilies and one unclassified gene. Throughout evolution, the subfamilies 5, 9, and 18 may have experienced stronger expansion. The segmental duplications may have contributed significantly to the expansion of the bHLH family. To systematically analyze the evolutionary relationships of the bHLH family in different plants, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. Finally, the gene expression response characteristics of 22 ScbHLH genes in various biological processes and stress responses were analyzed. Some candidate genes, such as ScbHLH11, ScbHLH48, and ScbHLH172, related to tissue developments and environmental stresses were screened. CONCLUSIONS The results indicate that these ScbHLH genes exhibit characteristic expression in different tissues, grain development stages, and stress treatments. These findings provided a basis for a comprehensive understanding of the bHLH family in rye.
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Affiliation(s)
- Xingyu Chen
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Caimei Yao
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Jiahao Liu
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Jintao Liu
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Jingmei Fang
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Hong Deng
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Qian Yao
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Tairan Kang
- School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China.
| | - Xiaoqiang Guo
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China.
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Sun M, Yao C, Shu Q, He Y, Chen G, Yang G, Xu S, Liu Y, Xue Z, Wu J. Telomere-to-telomere pear ( Pyrus pyrifolia) reference genome reveals segmental and whole genome duplication driving genome evolution. HORTICULTURE RESEARCH 2023; 10:uhad201. [PMID: 38023478 PMCID: PMC10681005 DOI: 10.1093/hr/uhad201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/01/2023] [Indexed: 12/01/2023]
Abstract
Previously released pear genomes contain a plethora of gaps and unanchored genetic regions. Here, we report a telomere-to-telomere (T2T) gap-free genome for the red-skinned pear, 'Yunhong No. 1' (YH1; Pyrus pyrifolia), which is mainly cultivated in Yunnan Province (southwest China), the pear's primary region of origin. The YH1 genome is 501.20 Mb long with a contig N50 length of 29.26 Mb. All 17 chromosomes were assembled to the T2T level with 34 characterized telomeres. The 17 centromeres were predicted and mainly consist of centromeric-specific monomers (CEN198) and long terminal repeat (LTR) Gypsy elements (≥74.73%). By filling all unclosed gaps, the integrity of YH1 is markedly improved over previous P. pyrifolia genomes ('Cuiguan' and 'Nijisseiki'). A total of 1531 segmental duplication (SD) driven duplicated genes were identified and enriched in stress response pathways. Intrachromosomal SDs drove the expansion of disease resistance genes, suggesting the potential of SDs in adaptive pear evolution. A large proportion of duplicated gene pairs exhibit dosage effects or sub-/neo-functionalization, which may affect agronomic traits like stone cell content, sugar content, and fruit skin russet. Furthermore, as core regulators of anthocyanin biosynthesis, we found that MYB10 and MYB114 underwent various gene duplication events. Multiple copies of MYB10 and MYB114 displayed obvious dosage effects, indicating role differentiation in the formation of red-skinned pear fruit. In summary, the T2T gap-free pear genome provides invaluable resources for genome evolution and functional genomics.
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Affiliation(s)
- Manyi Sun
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Chenjie Yao
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Qun Shu
- Institute of Horticulture, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Yingyun He
- Institute of Horticulture, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Guosong Chen
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Guangyan Yang
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Shaozhuo Xu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Yueyuan Liu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Zhaolong Xue
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
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Guerra D, Morcia C, Badeck F, Rizza F, Delbono S, Francia E, Milc JA, Monostori I, Galiba G, Cattivelli L, Tondelli A. Extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:553-569. [PMID: 34757472 PMCID: PMC8866391 DOI: 10.1007/s00122-021-03985-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/26/2021] [Indexed: 05/24/2023]
Abstract
Exome sequencing-based allele mining for frost tolerance suggests HvCBF14 rather than CNV at Fr-H2 locus is the main responsible of frost tolerance in barley. Wild relatives, landraces and old cultivars of barley represent a reservoir of untapped and potentially important genes for crop improvement, and the recent sequencing technologies provide the opportunity to mine the existing genetic diversity and to identify new genes/alleles for the traits of interest. In the present study, we use frost tolerance and vernalization requirement as case studies to demonstrate the power of allele mining carried out on exome sequencing data generated from > 400 barley accessions. New deletions in the first intron of VRN-H1 were identified and linked to a reduced vernalization requirement, while the allelic diversity of HvCBF2a, HvCBF4b and HvCBF14 was investigated by combining the analysis of SNPs and read counts. This approach has proven very effective to identify gene paralogs and copy number variants of HvCBF2 and the HvCBF4b-HvCBF2a segment. A multiple linear regression model which considers allelic variation at these genes suggests a major involvement of HvCBF14, rather than copy number variation of HvCBF4b-HvCBF2a, in controlling frost tolerance in barley. Overall, the present study provides powerful resource and tools to discover novel alleles at relevant genes in barley.
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Affiliation(s)
- Davide Guerra
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy.
| | - Caterina Morcia
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
| | - Franz Badeck
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
| | - Fulvia Rizza
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
| | - Stefano Delbono
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
| | - Enrico Francia
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad. Besta, 42122, Reggio Emilia, Italy
| | - Justyna Anna Milc
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad. Besta, 42122, Reggio Emilia, Italy
| | - Istvan Monostori
- Centre for Agricultural Research, Agricultural Institute, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
| | - Gabor Galiba
- Centre for Agricultural Research, Agricultural Institute, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
- Department of Environmental Sustainability, Festetics Doctoral School, IES, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Keszthely, 8360, Hungary
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
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Almerekova S, Genievskaya Y, Abugalieva S, Sato K, Turuspekov Y. Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data. PLANTS 2021; 10:plants10102025. [PMID: 34685834 PMCID: PMC8540147 DOI: 10.3390/plants10102025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/17/2021] [Accepted: 09/24/2021] [Indexed: 12/22/2022]
Abstract
The genetic relationship and population structure of two-rowed barley accessions from Kazakhstan were assessed using single-nucleotide polymorphism (SNP) markers. Two different approaches were employed in the analysis: (1) the accessions from Kazakhstan were compared with barley samples from six different regions around the world using 1955 polymorphic SNPs, and (2) 94 accessions collected from six breeding programs from Kazakhstan were studied using 5636 polymorphic SNPs using a 9K Illumina Infinium assay. In the first approach, the neighbor-joining tree showed that the majority of the accessions from Kazakhstan were grouped in a separate subcluster with a common ancestral node; there was a sister subcluster that comprised mainly barley samples that originated in Europe. The Pearson’s correlation analysis suggested that Kazakh accessions were genetically close to samples from Africa and Europe. In the second approach, the application of the STRUCTURE package using 5636 polymorphic SNPs suggested that Kazakh barley samples consisted of five subclusters in three major clusters. The principal coordinate analysis plot showed that, among six breeding origins in Kazakhstan, the Krasnovodopad (KV) and Karaganda (KA) samples were the most distant groups. The assessment of the pedigrees in the KV and KA samples showed that the hybridization schemes in these breeding stations heavily used accessions from Ethiopia and Ukraine, respectively. The comparative analysis of the KV and KA samples allowed us to identify 214 SNPs with opposite allele frequencies that were tightly linked to 60 genes/gene blocks associated with plant adaptation traits, such as the heading date and plant height. The identified SNP markers can be efficiently used in studies of barley adaptation and deployed in breeding projects to develop new competitive cultivars.
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Affiliation(s)
- Shyryn Almerekova
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (Y.G.); (S.A.)
- Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
| | - Yuliya Genievskaya
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (Y.G.); (S.A.)
- Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
| | - Saule Abugalieva
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (Y.G.); (S.A.)
- Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan;
| | - Yerlan Turuspekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (Y.G.); (S.A.)
- Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
- Correspondence:
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Xie Y, Ravet K, Pearce S. Extensive structural variation in the Bowman-Birk inhibitor family in common wheat (Triticum aestivum L.). BMC Genomics 2021; 22:218. [PMID: 33765923 PMCID: PMC7995804 DOI: 10.1186/s12864-021-07475-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bowman-Birk inhibitors (BBI) are a family of serine-type protease inhibitors that modulate endogenous plant proteolytic activities during different phases of development. They also inhibit exogenous proteases as a component of plant defense mechanisms, and their overexpression can confer resistance to phytophagous herbivores and multiple fungal and bacterial pathogens. Dicot BBIs are multifunctional, with a "double-headed" structure containing two separate inhibitory loops that can bind and inhibit trypsin and chymotrypsin proteases simultaneously. By contrast, monocot BBIs have a non-functional chymotrypsin inhibitory loop, although they have undergone internal duplication events giving rise to proteins with multiple BBI domains. RESULTS We used a Hidden Markov Model (HMM) profile-based search to identify 57 BBI genes in the common wheat (Triticum aestivum L.) genome. The BBI genes are unevenly distributed, with large gene clusters in the telomeric regions of homoeologous group 1 and 3 chromosomes that likely arose through a series of tandem gene duplication events. The genomes of wheat progenitors also contain contiguous clusters of BBI genes, suggesting this family underwent expansion before the domestication of common wheat. However, the BBI gene family varied in size among different cultivars, showing this family remains dynamic. Because of these expansions, the BBI gene family is larger in wheat than other monocots such as maize, rice and Brachypodium. We found BBI proteins in common wheat with intragenic homologous duplications of cysteine-rich functional domains, including one protein with four functional BBI domains. This diversification may expand the spectrum of target substrates. Expression profiling suggests that some wheat BBI proteins may be involved in regulating endogenous proteases during grain development, while others were induced in response to biotic and abiotic stresses, suggesting a role in plant defense. CONCLUSIONS Genome-wide characterization reveals that the BBI gene family in wheat is subject to a high rate of homologous tandem duplication and deletion events, giving rise to a diverse set of encoded proteins. This information will facilitate the functional characterization of individual wheat BBI genes to determine their role in wheat development and stress responses, and their potential application in breeding.
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Affiliation(s)
- Yucong Xie
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Karl Ravet
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
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