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Wang C, Bao Y, Yao Q, Long D, Xiao X, Fan X, Kang H, Zeng J, Sha L, Zhang H, Wu D, Zhou Y, Zhou Q, Wang Y, Cheng Y. Fine mapping of the reduced height gene Rht22 in tetraploid wheat landrace Jianyangailanmai (Triticum turgidum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3643-3660. [PMID: 36057866 DOI: 10.1007/s00122-022-04207-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Rht22 was fine mapped in the interval of 0.53-1.48 Mb on 7AS, which reduces cell number of internode to cause semi-dwarfism in Jianyangailanmai. As a valuable germplasm resource for wheat genetic improvement, tetraploid wheat has several reduced height (Rht) and enhanced harvest index genes. Rht22, discovered in Jianyangailanmai (JAM, Triticum turgidum L., 2n = 4x = 28, AABB), significantly increases the spikelet number per spike, but its accurate chromosomal position is still unknown. In this study, a high-density genetic map was constructed using specific-length amplified fragment sequencing in an F7 RIL_DJ population, which was derived from a cross between dwarf Polish wheat (T. polonicum L., 2n = 4x = 28, AABB) and JAM. Two plant height loci, Qph.sicau-4B and Qph.sicau-7A, were mapped on chromosomes 4BS and 7AS, respectively. Qph.sicau-7A was mapped to the 0.33-4.46 Mb interval on 7AS and likely represents the candidate region of Rht22. Fine mapping confirmed and narrowed Rht22 on chromosome arm 7AS between Xbag295.s53 and Xb295.191 in three different populations. The physical region ranged from 0.53 to 1.48 Mb and included 18 candidate genes. Transcriptome analysis of two pairs of near-isogenic lines revealed that 135 differentially expressed genes (DEGs) were associated with semi-dwarfism. Of these, the expression of 83 annotated DEGs involved in hormones synthesis and signal transduction, cell wall composition, DNA replication, microtubule and phragmoplast arrays was significantly down-regulated in the semi-dwarf line. Therefore, Rht22 causes semi-dwarfism in JAM by disrupting these cellular processes, which impairs cell proliferation and reduces internode cell number.
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Affiliation(s)
- Chao Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yunjing Bao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Qin Yao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Dan Long
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Xue Xiao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, 610041, Sichuan, China.
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
| | - Yiran Cheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
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Chen Z, Liao M, Yang Z, Chen W, Wei S, Zou J, Peng Z. Co-expression network analysis of genes and networks associated with wheat pistillody. PeerJ 2022; 10:e13902. [PMID: 36039368 PMCID: PMC9419718 DOI: 10.7717/peerj.13902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/24/2022] [Indexed: 01/19/2023] Open
Abstract
Crop male sterility has great value in theoretical research and breeding application. HTS-1, whose stamens transformed into pistils or pistil-like structures, is an important male sterility material selecting from Chinese Spring three-pistil (CSTP) wheat. However the molecular mechanism of pistillody development in HTS-1 remains a mystery. RNA-seq data of 11 wheat tissues were obtained from the National Center for Biotechnology Information (NCBI), including the stamens of CSTP and the pistils and pistillodic stamen of HTS-1. The Salmon program was utilized to quantify the gene expression levels of the 11 wheat tissues; and gene quantification results were normalized by transcripts per million (TPM). In total, 58,576 genes were used to construct block-wise network by co-expression networks analysis (WGCNA) R package. We obtained all of modules significantly associated with the 11 wheat tissues. AgriGO V2.0 was used to do Gene Ontology (GO) enrichment analysis; and genes and transcription factors (TFs) in these significant modules about wheat pistillody development were identified from GO enrichment results. Basic local alignment search tool (BLAST) was used to align HTS-1 proteins with the published pistillody-related proteins and TFs. Genes about wheat pistillody development were analyzed and validated by qRT-PCR. The MEturquoise, MEsaddlebrown, MEplum, MEcoral1, MElightsteelblue1, and MEdarkslateblue modules were significantly corelated to pistillodic stamen (correlation p < 0.05). Moreover, 206 genes related to carpel development (GO:0048440) or gynoecium development (GO:0048467) were identified only in the MEturquoise module by Gene Ontology (GO) analysis, and 42 of 206 genes were hub genes in MEturquoise module. qRT-PCR results showed that 38 of the 42 hub genes had highly expressed in pistils and pistillodic stamens than in stamens. A total of 15 pistillody development-related proteins were validated by BLAST. Transcription factors (TFs) were also analyzed in the MEturquoise module, and 618 TFs were identified. In total, 56 TFs from 11 families were considered to regulate the development of pistillodic stamen. The co-expression network showed that six of HB and three of BES1 genes were identified in 42 hub genes. This indicated that TFs played important roles in wheat pistillody development. In addition, there were 11 of ethylene-related genes connected with TFs or hub genes, suggesting the important roles of ethylene-related genes in pistillody development. These results provide important insights into the molecular interactions underlying pistillody development.
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Affiliation(s)
- Zhenyong Chen
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, Sichuan, People’s Republic of China
| | - Mingli Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, Sichuan, People’s Republic of China
| | - Zaijun Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, Sichuan, People’s Republic of China
| | - Weiying Chen
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, Sichuan, People’s Republic of China
| | - Shuhong Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, Sichuan, People’s Republic of China
| | - Jian Zou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, Sichuan, People’s Republic of China
| | - Zhengsong Peng
- School of Agricultural Science, Xichang University, Xichang, Sichuan, People’s Republic of China
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Gubaev R, Boldyrev S, Martynova E, Chernova A, Kovalenko T, Peretyagina T, Goryunova S, Goryunov D, Mukhina Z, Ben C, Gentzbittel L, Khaitovich P, Demurin Y. Genetic mapping of loci involved in oil tocopherol composition control in Russian sunflower ( Helianthus annuus L.) lines. G3 GENES|GENOMES|GENETICS 2022; 12:6527637. [PMID: 35150257 PMCID: PMC8982403 DOI: 10.1093/g3journal/jkac036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/25/2022] [Indexed: 11/14/2022]
Abstract
Abstract
Tocopherols are antioxidants that preserve oil lipids against oxidation and serve as a natural source of vitamin E in the human diet. Compared with other major oilseeds like rapeseed and soybean, sunflower (Helianthus annuus L.) exhibits low phenotypic diversity of tocopherol composition, both in wild and cultivated accessions from germplasm collections. Two major mutations that alter tocopherol composition were identified in genetic collections, and several studies suggested additional loci controlling tocopherol composition, with their expression possibly depending on the genetic background. In the present study, we performed QTL mapping of tocopherol composition in two independent F2 crosses between lines with contrasting tocopherol composition from the Pustovoit All-Russia Research Institute of Oil Crops (VNIIMK) collection. We used genotyping-bysequencing (GBS) to construct single nucleotide polymorphism-based genetic maps, and performed QTL mapping using quantitative and qualitative encoding for phenotypic traits. Our results support the notion that the tocopherol composition in the assessed crosses is controlled by two loci. We additionally selected and validated two single nucleotide polymorphism markers for each cross which could be used for marker-assisted selection.
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Affiliation(s)
- Rim Gubaev
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- LLC “Oil Gene”, Moscow 121205, Russia
| | - Stepan Boldyrev
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- LLC “Oil Gene”, Moscow 121205, Russia
| | - Elena Martynova
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Alina Chernova
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- LLC “Oil Gene”, Moscow 121205, Russia
| | - Tatyana Kovalenko
- Pustovoit All-Russia Research Institute of Oil Crops, Krasnodar 350038, Russia
| | - Tatyana Peretyagina
- Pustovoit All-Russia Research Institute of Oil Crops, Krasnodar 350038, Russia
| | - Svetlana Goryunova
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Russian Potato Research Center, Kraskovo 140051, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia
| | - Denis Goryunov
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Zhanna Mukhina
- All-Russia Rice Research Institute, Krasnodar 350921, Russia
| | - Cecile Ben
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | | | | | - Yakov Demurin
- Pustovoit All-Russia Research Institute of Oil Crops, Krasnodar 350038, Russia
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Yu Y, Yang Z, Jiang Y, Wang L, Wu Y, Liao J, Yang R, Zhang L. Inheritance and QTL Mapping for Flower Color in Salvia miltiorrhiza Bunge. J Hered 2022; 113:248-256. [PMID: 35259262 DOI: 10.1093/jhered/esac012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/04/2022] [Indexed: 11/12/2022] Open
Abstract
Salvia miltiorrhiza Bunge is an outcross-pollinated plant with diverse flower colors, ranging from white to purple. To clarify the genetic basis of S. miltiorrhiza flower color, we crossed white-flowered S. miltiorrhiza f. alba with dark violet-flowered S. miltiorrhiza, and selfed F1 to obtain an F2 population. The RGB color system was used to describe the flower color of the parents, F1 progeny, and F2 individuals. Afterward, we used genotyping-by-sequencing (GBS) technology to construct a high-density linkage map of S. miltiorrhiza based on the F2 population. Finally, the linkage map was used to locate the QTLs of the genes that control flower color in S. miltiorrhiza. Through measurement and cluster analysis of the R, G, and B values of flowers from the parents, F1, and F2 individuals, it was found that the purple flower color of S. miltiorrhiza is a quantitative trait controlled by two loci of major genes. The genetic map contained 605 SNPs with a total length of 738.3 cM in eight linkage groups (LGs), and the average distance between two markers was 1.22 cM. Based on the constructed genetic map and the flower R, G, B, and R+G+B values, two QTLs were detected for flower color, located on LG4 and LG5. The results of this study lay the foundation for cloning genes that control flower color and studying the molecular mechanism of flower color regulation in S. miltiorrhiza.
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Affiliation(s)
- Yan Yu
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Zaijun Yang
- College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Yuanyuan Jiang
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Long Wang
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Yichao Wu
- College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Jinqiu Liao
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Ruiwu Yang
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Li Zhang
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
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Mishra A, Singh A, Mantri S, Pandey AK, Garg M, Deshmukh R, Sonah H, Kandoth PK, Sharma TR, Roy J. Decoding the genome of superior chapatti quality Indian wheat variety 'C 306' unravelled novel genomic variants for chapatti and nutrition quality related genes. Genomics 2021; 113:1919-1929. [PMID: 33823224 DOI: 10.1016/j.ygeno.2021.03.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/18/2021] [Accepted: 03/29/2021] [Indexed: 11/26/2022]
Abstract
An Indian wheat variety, 'C 306' has good chapatti quality, which is controlled by multiple genes that have not been explored. We report the high quality de novo assembled genome of 'C 306' by combining short and long read sequencing data. The hybrid assembly covered 93% of gene space and identified about 142 K coding genes, 34% repetitive DNA and ~ 501 K SSR motifs. The phylogenetic analysis of about 83 K orthologous protein groups suggested the closest relationship with T. turgidum, T. aestivum and Ae. tauschii. Genome wide analysis annotated 69,217,536 genomic variants. Out of them, 1423 missense and 117 deleterious variants identified in processing, nutrition, and chapatti quality related genes such as alpha- and beta-gliadin, SSI, SSIII, SUT1, SBEI, CHS, YSL, DMAS, and NAS encoded proteins. These variants may affect quality genes. The genomic data will be potential genomic resources in wheat breeding programs for quality improvement.
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Affiliation(s)
- Ankita Mishra
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, Punjab, India.
| | - Akshay Singh
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, Punjab, India.
| | - Shrikant Mantri
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, Punjab, India.
| | - Ajay K Pandey
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, Punjab, India.
| | - Monika Garg
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, Punjab, India.
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, Punjab, India.
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, Punjab, India.
| | | | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, Punjab, India.
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, Punjab, India.
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An SNP-Based High-Density Genetic Linkage Map for Tetraploid Potato Using Specific Length Amplified Fragment Sequencing (SLAF-Seq) Technology. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10010114] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for the discovery of large-scale de novo genotyping of single nucleotide polymorphism (SNP) markers. In the present research, in order to facilitate genome-guided breeding in potato, this strategy was used to develop a large number of SNP markers and construct a high-density genetic linkage map for tetraploid potato. The genomic DNA extracted from 106 F1 individuals derived from a cross between two tetraploid potato varieties YSP-4 × MIN-021 and their parents was used for high-throughput sequencing and SLAF library construction. A total of 556.71 Gb data, which contained 2269.98 million pair-end reads, were obtained after preprocessing. According to bioinformatics analysis, a total of 838,604 SLAF labels were developed, with an average sequencing depth of 26.14-fold for parents and 15.36-fold for offspring of each SLAF, respectively. In total, 113,473 polymorphic SLAFs were obtained, from which 7638 SLAFs were successfully classified into four segregation patterns. After filtering, a total of 7329 SNP markers were detected for genetic map construction. The final integrated linkage map of tetraploid potato included 3001 SNP markers on 12 linkage groups, and covered 1415.88 cM, with an average distance of 0.47 cM between adjacent markers. To our knowledge, the integrated map described herein has the best coverage of the potato genome and the highest marker density for tetraploid potato. This work provides a foundation for further quantitative trait loci (QTL) location, map-based gene cloning of important traits and marker-assisted selection (MAS) of potato.
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Sun Q, Qu J, Yu Y, Yang Z, Wei S, Wu Y, Yang J, Peng Z. TaEPFL1, an EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) secreted peptide gene, is required for stamen development in wheat. Genetica 2019; 147:121-130. [PMID: 30911860 DOI: 10.1007/s10709-019-00061-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/20/2019] [Indexed: 11/26/2022]
Abstract
Members of the EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family play diverse roles in plant growth and development, including the guidance of inflorescence architecture and pedicel length. In this work, we identified and characterized the EFPL gene TaEPFL1 from the wheat pistillody mutant HTS-1. Sequence alignment and phylogenetic analysis indicated that TaEPFL1 belongs to the EPFL1 gene. Quantitative real-time RT-PCR analysis showed that the TaEPFL1 gene is expressed at an abnormally high level in pistillody stamens compared with that in pistils and stamens. Heterologous expression of the TaEPFL1 gene in Arabidopsis caused shortened filaments and pedicels and might reduce the level of AtACO2 gene expression. These results suggest that TaEPFL1 plays an important role in the development of stamen and that overexpression of TaEPFL1 results in abnormal stamens. We deduced that the overexpression of the TaEPFL1 gene may contribute to the homeotic transformation of stamens into pistils or pistil-like structures in wheat. These data offer insights into the molecular mechanism of pistillody mutation in wheat.
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Affiliation(s)
- Qingxu Sun
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, People's Republic of China
| | - Jipeng Qu
- School of Agricultural Science, Xichang University, Xichang, 615000, Sichuan, People's Republic of China
| | - Yan Yu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, People's Republic of China
| | - Zaijun Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, People's Republic of China.
| | - Shuhong Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, People's Republic of China
| | - Yilei Wu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, People's Republic of China
| | - Jun Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, People's Republic of China
| | - Zhengsong Peng
- School of Agricultural Science, Xichang University, Xichang, 615000, Sichuan, People's Republic of China
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