1
|
Yu JY, Zhang ZG, Huang SY, Han X, Wang XY, Pan WJ, Qin HT, Qi HD, Yin ZG, Qu KX, Zhang ZX, Liu SS, Jiang HW, Liu CY, Hu ZB, Wu XX, Chen QS, Xin DW, Qi ZM. Analysis of miRNAs Targeted Storage Regulatory Genes during Soybean Seed Development Based on Transcriptome Sequencing. Genes (Basel) 2019; 10:E408. [PMID: 31142023 PMCID: PMC6628032 DOI: 10.3390/genes10060408] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 01/05/2023] Open
Abstract
Soybeans are an important cash crop and are widely used as a source of vegetable protein and edible oil. MicroRNAs (miRNA) are endogenous small RNA that play an important regulatory role in the evolutionarily conserved system of gene expression. In this study, we selected four lines with extreme phenotypes, as well as high or low protein and oil content, from the chromosome segment substitution line (CSSL) constructed from suinong (SN14) and ZYD00006, and planted and sampled at three stages of grain development for small RNA sequencing and expression analysis. The sequencing results revealed the expression pattern of miRNA in the materials, and predicted miRNA-targeted regulatory genes, including 1967 pairs of corresponding relationships between known-miRNA and their target genes, as well as 597 pairs of corresponding relationships between novel-miRNA and their target genes. After screening and annotating genes that were targeted for regulation, five specific genes were identified to be differentially expressed during seed development and subsequently analyzed for their regulatory relationship with miRNAs. The expression pattern of the targeted gene was verified by Real-time Quantitative PCR (RT-qPCR). Our research provides more information about the miRNA regulatory network in soybeans and further identifies useful genes that regulate storage during soy grain development, providing a theoretical basis for the regulation of soybean quality traits.
Collapse
Affiliation(s)
- Jing-Yao Yu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Zhan-Guo Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Shi-Yu Huang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Xue Han
- Department of Horticulture, Michigan State University, East Lansing 48824, MI, USA.
| | - Xin-Yu Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Wen-Jing Pan
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Hong-Tao Qin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Hui-Dong Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Zhen-Gong Yin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Ke-Xin Qu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Ze-Xin Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Shan-Shan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Hong-Wei Jiang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Chun-Yan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Zhen-Bang Hu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Xiao-Xia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
- Green Food Research Institute in Heilongjiang Province, Harbin 150030, Heilongjiang, China.
| | - Qing-Shan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Da-Wei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Zhao-Ming Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
- Department of Plant Soil and Microbe Science, Michigan State University, East Lansing, MI 48824, USA.
| |
Collapse
|
2
|
Zhang HM, Xia HL, Jiang HR, Mao YJ, Qu KX, Huang BZ, Gong YC, Yang ZP. Longissimus dorsi muscle transcriptomic analysis of Yunling and Chinese simmental cattle differing in intramuscular fat content and fatty acid composition. Genome 2018; 61:549-558. [PMID: 29883552 DOI: 10.1139/gen-2017-0164] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Intramuscular fat (IMF) content and fatty acid (FA) composition vary significantly across beef cattle breeds, which play an important role in taste and nutritional value. However, the molecular mechanisms underlying these phenotypic differences remain unknown. The present study compared meat quality traits between Yunling cattle and Chinese Simmental cattle. Yunling cattle showed a lower IMF content and proportion of monounsaturated fatty acids (MUFA), as well as higher proportions of saturated fatty acids (SFA), polyunsaturated fatty acids (PUFA), and short-chain fatty acids (sc-FA) in the longissimus dorsi (LD) muscle than Chinese Simmental cattle. To further identify the candidate genes and pathways responsible for these phenotypic differences, the transcriptome of LD muscle from the two breeds were measured using RNA-seq. A total of 1347 differentially expressed genes were identified. The major metabolic pathways that were differentially modulated were lipolysis and glycometabolism. Yunling cattle showed a higher expression of lipolysis genes (ALDH9A1, ACSL5, ACADM, ACAT2, ACOT2) and a lower expression of genes related to glycometabolism (PGM1, GALM, PGM1, GPI, LDHA). This research identified candidate genes and pathways for IMF content and FA composition in the LD muscle of beef cattle, which may facilitate the design of new selection strategies to improve meat quality.
Collapse
Affiliation(s)
- H M Zhang
- a Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.,b Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - H L Xia
- a Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.,b Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - H R Jiang
- a Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.,b Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Y J Mao
- a Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.,b Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - K X Qu
- c Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan 650212, China
| | - B Z Huang
- c Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan 650212, China
| | - Y C Gong
- d The Centre for the Analysis of Genome Evolution and Function (CAGEF), University of Toronto, Toronto, ON M5S 2J7, Canada
| | - Z P Yang
- a Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.,b Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
3
|
Qu KX, Huang BZ, Yang GR, He ZX, Zhang YP, Zan LS. Genetic diversity analysis of BMY cattle based on microsatellite DNA markers. Genetika 2012; 48:522-528. [PMID: 22730772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BMY cattle (1/2 Brahman, 1/4 Murray Grey and 1/4 Yunnan Yellow cattle) has been inter se breeding since 1980s. Genetic diversity of BMY cattle was extensively investigated using 16 microsatellite markers. A total of 130 microsatellite alleles and high allele size variance were detected. All loci displayed high genetic diversity with overall mean of N(a) = 8.13, PIC = 0.7224 and H(e) = 0.7666, which were higher than those of many other beef breeds. The allele-sharing neighbour-joining tree clearly displayed the new genotypic combinations and the minglement from both BMY cattle and Brahman. The results provided the genetic information to match the standards of new beef breed in South China.
Collapse
Affiliation(s)
- K X Qu
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | | | | | | | | | | |
Collapse
|