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Chachar Z, Lai R, Ahmed N, Lingling M, Chachar S, Paker NP, Qi Y. Cloned genes and genetic regulation of anthocyanin biosynthesis in maize, a comparative review. FRONTIERS IN PLANT SCIENCE 2024; 15:1310634. [PMID: 38328707 PMCID: PMC10847539 DOI: 10.3389/fpls.2024.1310634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/02/2024] [Indexed: 02/09/2024]
Abstract
Anthocyanins are plant-based pigments that are primarily present in berries, grapes, purple yam, purple corn and black rice. The research on fruit corn with a high anthocyanin content is not sufficiently extensive. Considering its crucial role in nutrition and health it is vital to conduct further studies on how anthocyanin accumulates in fruit corn and to explore its potential for edible and medicinal purposes. Anthocyanin biosynthesis plays an important role in maize stems (corn). Several beneficial compounds, particularly cyanidin-3-O-glucoside, perlagonidin-3-O-glucoside, peonidin 3-O-glucoside, and their malonylated derivatives have been identified. C1, C2, Pl1, Pl2, Sh2, ZmCOP1 and ZmHY5 harbored functional alleles that played a role in the biosynthesis of anthocyanins in maize. The Sh2 gene in maize regulates sugar-to-starch conversion, thereby influencing kernel quality and nutritional content. ZmCOP1 and ZmHY5 are key regulatory genes in maize that control light responses and photomorphogenesis. This review concludes the molecular identification of all the genes encoding structural enzymes of the anthocyanin pathway in maize by describing the cloning and characterization of these genes. Our study presents important new understandings of the molecular processes behind the manufacture of anthocyanins in maize, which will contribute to the development of genetically modified variants of the crop with increased color and possible health advantages.
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Affiliation(s)
- Zaid Chachar
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - RuiQiang Lai
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Nazir Ahmed
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Ma Lingling
- College of Agriculture, Jilin Agricultural University, Changchun, Jilin, China
| | - Sadaruddin Chachar
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | | | - YongWen Qi
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Shim KC, Kang Y, Song JH, Kim YJ, Kim JK, Kim C, Tai TH, Park I, Ahn SN. A Frameshift Mutation in the Mg-Chelatase I Subunit Gene OsCHLI Is Associated with a Lethal Chlorophyll-Deficient, Yellow Seedling Phenotype in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2831. [PMID: 37570985 PMCID: PMC10420988 DOI: 10.3390/plants12152831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/23/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
Chlorophyll biosynthesis is a crucial biological process in plants, and chlorophyll content is one of the most important traits in rice breeding programs. In this study, we identified a lethal, chlorophyll-deficient, yellow seedling (YS) phenotype segregating in progeny of CR5055-21, an F2 plant derived from a backcross between Korean japonica variety 'Hwaseong' (Oryza sativa) and CR5029, which is mostly Hwaseong with a small amount of Oryza grandiglumis chromosome segments. The segregation of the mutant phenotype was consistent with a single gene recessive mutation. Light microscopy of YS leaf cross-sections revealed loosely arranged mesophyll cells and sparse parenchyma in contrast to wildtype. In addition, transmission electron microscopy showed that chloroplasts did not develop in the mesophyll cells of the YS mutant. Quantitative trait loci (QTL)-seq analysis did not detect any significant QTL, however, examination of the individual delta-SNP index identified a 2-bp deletion (AG) in the OsCHLI gene, a magnesium (Mg)-chelatase subunit. A dCAPs marker was designed and genotyping of a segregating population (n = 275) showed that the mutant phenotype co-segregated with the marker. The 2-bp deletion was predicted to result in a frameshift mutation generating a premature termination. The truncated protein likely affects formation and function of Mg-chelatase, which consists of three different subunits that together catalyze the first committed step of chlorophyll biosynthesis. Transcriptome analysis showed that photosynthesis and carbohydrate metabolism pathways were significantly altered although expression of OsCHLI was not. Chlorophyll- and carotenoid-related genes were also differentially expressed in the YS mutant. Our findings demonstrated that OsCHLI plays an important role in leaf pigment biosynthesis and leaf structure development in rice.
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Affiliation(s)
- Kyu-Chan Shim
- Department of Agronomy, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Republic of Korea; (K.-C.S.); (Y.K.); (C.K.)
- USDA-ARS Crops Pathology and Genetics Research Unit, Davis, CA 95616, USA;
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Yuna Kang
- Department of Agronomy, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Republic of Korea; (K.-C.S.); (Y.K.); (C.K.)
| | - Jun-Ho Song
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea;
| | - Ye Jin Kim
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea; (Y.J.K.); (J.K.K.)
| | - Jae Kwang Kim
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea; (Y.J.K.); (J.K.K.)
| | - Changsoo Kim
- Department of Agronomy, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Republic of Korea; (K.-C.S.); (Y.K.); (C.K.)
| | - Thomas H. Tai
- USDA-ARS Crops Pathology and Genetics Research Unit, Davis, CA 95616, USA;
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Inkyu Park
- Department of Biology and Chemistry, Changwon National University, Changwon 51140, Republic of Korea
| | - Sang-Nag Ahn
- Department of Agronomy, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Republic of Korea; (K.-C.S.); (Y.K.); (C.K.)
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Zou T, Wang X, Sun T, Rong H, Wu L, Deng J, Guo T, Wang H, Wang J, Huang M. MYB Transcription Factor OsC1PLSr Involves the Regulation of Purple Leaf Sheath in Rice. Int J Mol Sci 2023; 24:ijms24076655. [PMID: 37047628 PMCID: PMC10095077 DOI: 10.3390/ijms24076655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
Although several regulators associated with purple traits in rice have been identified, the genetic basis of the purple sheath remains unclear. In the present study, F2-1 and F2-2 populations were constructed using purple sheath (H93S) and green sheath (R1173 and YHSM), respectively. In order to identify QTL loci in purple sheaths, BSA analyses were performed on the two F2 populations. A crucial QTL for purple sheath was identified, tentatively named qPLSr6, and was located in the 4.61 Mb to 6.03 Mb region of chromosome 6. Combined with expression pattern analysis of candidate genes, LOC_Os06g10350 (OsC1PLSr) was suggested as a candidate gene. The homozygous mutant KO-1 and KO-2 created through CRISPR/Cas9 editing, lost their purple leaf sheath. The RT-PCR revealed that OsC1PLSr, anthocyanin synthase (ANS), diflavonol-4-reductase (DFR), flavanone-3-hydroxylase (F3H), and flavanone-3′-hydroxylase (F3′H) expression levels were dramatically down-regulated in the mutants. The yeast report system indicated that the 145–272 aa region at the C-terminal of OsC1PLSr is a positive transcriptional activation domain. The results indicated that OsC1PLSr synthesized anthocyanins by regulating the expression of ANS, DFR, F3H, and F3′H. This study provides new insights into the genetic basis of the purple sheath.
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Affiliation(s)
- Ting Zou
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Xinyi Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Tong Sun
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Huazhen Rong
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Linxuan Wu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Jing Deng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Tao Guo
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Hui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Jiafeng Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Ming Huang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
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Shi T, Gao Y, Xu A, Wang R, Lyu M, Sun Y, Chen L, Liu Y, Luo R, Wang H, Liu J. A fast breeding strategy creates fragrance- and anthocyanin-enriched rice lines by marker-free gene-editing and hybridization. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:23. [PMID: 37313528 PMCID: PMC10248702 DOI: 10.1007/s11032-023-01369-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/06/2023] [Indexed: 06/15/2023]
Abstract
As rice is a staple food for nearly half of the world's population, rice varieties with excellent agronomic traits as well as high flavor and nutritional quality such as fragrant rice and purple rice are naturally favored by the market. In the current study, we adopt a fast breeding strategy to improve the aroma and anthocyanin content in the excellent rice inbred line, F25. The strategy skillfully used the advantages of obtaining editing pure lines in T0 generation of CRISPR/Cas9 editing system and easy observation of purple character and grain shape, integrated the subsequent screening of non-transgenic lines, and the elimination of undesirable edited variants from gene-editing and cross-breeding at the same time as the separation of the progeny from the purple cross, thus expediting the breeding process. Compared with conventional breeding strategies, this strategy saves about 6-8 generations and reduces breeding costs. Firstly, we edited the OsBADH2 gene associated with rice flavor using an Agrobacterium-mediated CRISPR/Cas9 system to improve the aroma of F25. In the T0 generation, a homozygous OsBADH2-edited F25 line (F25B) containing more of the scented substance 2-AP was obtained. Then, we crossed F25B (♀) with a purple rice inbred line, P351 (♂), with high anthocyanin enrichment to improve the anthocyanin content of F25. After nearly 2.5 years of screening and identification over five generations, the undesirable variation characteristics caused by gene-editing and hybridization and the transgenic components were screened out. Finally, the improved F25 line with highly stable aroma component, 2-AP, increased anthocyanin content and no exogenous transgenic components were obtained. This study not only provides high-quality aromatic anthocyanin rice lines that meet the market demand, but also offers a reference for the comprehensive use of CRISPR/Cas9 editing technology, hybridization, and marker-assisted selection to accelerate multi-trait improvement and breeding process. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01369-1.
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Affiliation(s)
- Tiantian Shi
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
| | - Ying Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
| | - Andi Xu
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
| | - Rui Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
| | - Mingjie Lyu
- Institute of Germplasm Resources and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, 300112 China
| | - Yinglu Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
| | - Luoying Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
- Tianjin Agricultural University, Tianjin, 300392 China
| | - Yuanhang Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
| | - Rong Luo
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 China
- Chengdu National Agricultural Science and Technology Center, Chengdu, 610213 Sichuan China
| | - Jun Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
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Cheng W, Wang Z, Xu F, Lu G, Su Y, Wu Q, Wang T, Que Y, Xu L. Screening of Candidate Genes Associated with Brown Stripe Resistance in Sugarcane via BSR-seq Analysis. Int J Mol Sci 2022; 23:ijms232415500. [PMID: 36555141 PMCID: PMC9778799 DOI: 10.3390/ijms232415500] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022] Open
Abstract
Sugarcane brown stripe (SBS), caused by the fungal pathogen Helminthosporium stenospilum, is one of the most serious threats to sugarcane production. However, its outbreaks and epidemics require suitable climatic conditions, resulting in the inefficient improvement of the SBS resistance by phenotype selection. The sugarcane F1 population of SBS-resistant YT93-159 × SBS-susceptible ROC22 was used for constructing the bulks. Bulked segregant RNA-seq (BSR-seq) was then performed on the parents YT93-159 (T01) and ROC22 (T02), and the opposite bulks of 30 SBS-susceptible individuals mixed bulk (T03) and 30 SBS-resistant individuals mixed bulk (T04) collected from 287 F1 individuals. A total of 170.00 Gb of clean data containing 297,921 SNPs and 70,426 genes were obtained. Differentially expressed genes (DEGs) analysis suggested that 7787 and 5911 DEGs were identified in the parents (T01 vs. T02) and two mixed bulks (T03 vs. T04), respectively. In addition, 25,363 high-quality and credible SNPs were obtained using the genome analysis toolkit GATK for SNP calling. Subsequently, six candidate regions with a total length of 8.72 Mb, which were located in the chromosomes 4B and 7C of sugarcane wild species Saccharum spontaneum, were identified, and 279 genes associated with SBS-resistance were annotated by ED algorithm and ΔSNP-index. Furthermore, the expression profiles of candidate genes were verified by quantitative real-time PCR (qRT-PCR) analysis, and the results showed that eight genes (LRR-RLK, DHAR1, WRKY7, RLK1, BLH4, AK3, CRK34, and NDA2) and seven genes (WRKY31, CIPK2, CKA1, CDPK6, PFK4, CBL2, and PR2) of the 20 tested genes were significantly up-regulated in YT93-159 and ROC22, respectively. Finally, a potential molecular mechanism of sugarcane response to H. stenospilum infection is illustrate that the activations of ROS signaling, MAPK cascade signaling, Ca2+ signaling, ABA signaling, and the ASA-GSH cycle jointly promote the SBS resistance in sugarcane. This study provides abundant gene resources for the SBS resistance breeding in sugarcane.
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Affiliation(s)
| | | | | | | | | | | | | | - Youxiong Que
- Correspondence: (Y.Q.); (L.X.); Tel.: +86-591-8385-2547 (Y.Q.); +86-591-8377-2604 (L.X.)
| | - Liping Xu
- Correspondence: (Y.Q.); (L.X.); Tel.: +86-591-8385-2547 (Y.Q.); +86-591-8377-2604 (L.X.)
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Combined Analysis of BSA-Seq Based Mapping, RNA-Seq, and Metabolomic Unraveled Candidate Genes Associated with Panicle Grain Number in Rice (Oryza sativa L.). Biomolecules 2022; 12:biom12070918. [PMID: 35883474 PMCID: PMC9313402 DOI: 10.3390/biom12070918] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 01/27/2023] Open
Abstract
Rice grain yield is a complex and highly variable quantitative trait consisting of several key components, including the grain weight, the effective panicles per unit area, and the grain number per panicle (GNPP). The GNPP is a significant contributor to grain yield controlled by multiple genes (QTL) and is crucial for improvement. Attempts have been made to find genes for this trait, which has always been a challenging and arduous task through conventional methods. We combined a BSA analysis, RNA profiling, and a metabolome analysis in the present study to identify new candidate genes involved in the GNPP. The F2 population from crossing R4233 (high GNPP) and Ce679 (low GNPP) revealed a frequency distribution fitting two segregated genes. Three pools, including low, middle, and high GNPP, were constructed and a BSA analysis revealed six candidate regions spanning 5.38 Mb, containing 739 annotated genes. Further, a conjunctive analysis of BSA-Seq and RNA-Seq showed 31 differentially expressed genes (DEGs) in the candidate intervals. Subsequently, a metabolome analysis showed 1024 metabolites, with 71 significantly enriched, including 44 up and 27 downregulated in Ce679 vs. R4233. A KEGG enrichment analysis of these 31 DEGs and 71 differentially enriched metabolites (DEMs) showed two genes, Os12g0102100 and Os01g0580500, significantly enriched in the metabolic pathways’ biosynthesis of secondary metabolites, cysteine and methionine metabolism, and fatty acid biosynthesis. Os12g0102100, which encodes for the alcohol dehydrogenase superfamily and a zinc-containing protein, is a novel gene whose contribution to the GNPP is not yet elucidated. This gene coding for mitochondrial trans-2-enoyl-CoA reductase is involved in the biosynthesis of myristic acid, also known as tetradecanoic acid. The Os01g0580500 coding for the enzyme 1-aminoclopropane-1-carboxylate oxidase (OsACO7) is responsible for the final step of the ethylene biosynthesis pathway through the conversion of 1-aminocyclopropane-1-carboxylic acid (ACC) into ethylene. Unlike Os12g0102100, this gene was significantly upregulated in R4233, downregulated in Ce679, and significantly enriched in two of the three metabolite pathways. This result pointed out that these two genes are responsible for the difference in the GNPP in the two cultivars, which has never been identified. Further validation studies may disclose the physiological mechanisms through which they regulate the GNPP in rice.
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Wang L, Liu Y, Zhao H, Zheng Y, Bai F, Deng S, Chen Z, Wu J, Liu X. Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping. FRONTIERS IN PLANT SCIENCE 2022; 13:921029. [PMID: 35783972 PMCID: PMC9240483 DOI: 10.3389/fpls.2022.921029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Grain length (GL) directly affects the yield and quality of rice. Very few cloned GL-related genes are applied in production because their yield-increasing effects are not obvious, and the overall regulatory networks underlying the associated processes remain poorly understood. DNA samples from two bulk DNA pools (L-pool and S-pool) and their parents (KJ01 and Huaye 3) were subjected to high-throughput sequencing. Using bulked segregant analysis (BSA), qGL3.5 was mapped to a 0.34-Mb "hotspot" region on chromosome 3 that contains 37 genes related to various traits. Then, qGL3.5 was mapped to the genomic interval between the flanking markers M2 and M3 using 2786 BC4F2 individuals. Because the region from B5 to B6 was not the associated region under BSA-seq analysis, qGL3.5 was narrowed down to the interval between B6 and M3, which spanned 24.0-kb. Of all 37 genes with non-synonymous single-nucleotide polymorphisms (SNPs) between KJ01 and Huaye 3 based on BSA-seq analysis, only one complete annotated gene, ORF18 (Gene ID: LOC_Os03g42790.1) was found. ORF18 encodes an IBR-RING zinc-finger-related protein, with one really interesting new gene (RING) and two in between ring finger (IBR) domains. The knockout of ORF18 derived from Huaye 3 using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) editing technology increased the GL of the mutant by approximately 2.2 mm. The novel locus qGL3.5 negatively regulated GL by promoting elongation of the longitudinal cell of the grain outer glume. These results provide a new genetic resource for rice grain shape breeding and a starting point for the functional characterization of the wild rice GL gene.
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Affiliation(s)
- Lan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Haiyan Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Songgang Middle School, Qingyuan, China
| | - Yuebin Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Feng Bai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Sicheng Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Zhixiong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
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He P, Wei P, Ma Y, Hu S, Yao J, Jiang X, Xu Y, Zhu P, Wei M, Jiang W, Peng J. Candidate sex-associated gene identification in Trachinotus ovatus (Carangidae) using an integrated SLAF-seq and bulked segregant analysis approach. Gene 2022; 809:146026. [PMID: 34687789 DOI: 10.1016/j.gene.2021.146026] [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: 01/29/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 12/16/2022]
Abstract
It is difficult to distinguish the sexes of Trachinotus ovatus based on appearance, and little data about sex-determining genes are available for this species. Here, we generated 200 F2 individuals using the parents R404 and R403. DNA samples were collected from 50 individuals of each sex and aggregated into sex-specific DNA pools. Specific-locus amplified fragment sequencing was integrated with bulked segregant analysis to detect candidate sex-associated genes. Approximately 3,153,153 high-quality single-nucleotide polymorphism (SNP) markers and 135,363 high-quality insertion-deletion (Indel) markers were generated. Six candidate regions within chromosome 14, encompassing 132 candidate genes, were identified as closely related to sex. Based on annotations, six genes (EVM0019817, EVM0004192, EVM0001445, EVM0005260, EVM0014734, and EVM0009626) were predicted to be closely associated with sex. These results present an efficient genetic mapping approach that lays a foundation for molecular sex discrimination in T. ovatus.
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Affiliation(s)
- Pingping He
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Pinyuan Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Yuan Ma
- Beibu Gulf University, Qinzhou 535000, China
| | - Shenhua Hu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Jiuxiang Yao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Xiaozhen Jiang
- Guangxi Agricultural Vocational College, Nanning 530007, China
| | - Youhou Xu
- Beibu Gulf University, Qinzhou 535000, China
| | - Peng Zhu
- Beibu Gulf University, Qinzhou 535000, China
| | - Mingli Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Weiming Jiang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, China.
| | - Jinxia Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, China.
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Li B, Zhang X, Liu Z, Wang L, Song L, Liang X, Dou S, Tu J, Shen J, Yi B, Wen J, Fu T, Dai C, Gao C, Wang A, Ma C. Genetic and Molecular Characterization of a Self-Compatible Brassica rapa Line Possessing a New Class II S Haplotype. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122815. [PMID: 34961286 PMCID: PMC8709392 DOI: 10.3390/plants10122815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 05/20/2023]
Abstract
Most flowering plants have evolved a self-incompatibility (SI) system to maintain genetic diversity by preventing self-pollination. The Brassica species possesses sporophytic self-incompatibility (SSI), which is controlled by the pollen- and stigma-determinant factors SP11/SCR and SRK. However, the mysterious molecular mechanism of SI remains largely unknown. Here, a new class II S haplotype, named BrS-325, was identified in a pak choi line '325', which was responsible for the completely self-compatible phenotype. To obtain the entire S locus sequences, a complete pak choi genome was gained through Nanopore sequencing and de novo assembly, which provided a good reference genome for breeding and molecular research in B. rapa. S locus comparative analysis showed that the closest relatives to BrS-325 was BrS-60, and high sequence polymorphism existed in the S locus. Meanwhile, two duplicated SRKs (BrSRK-325a and BrSRK-325b) were distributed in the BrS-325 locus with opposite transcription directions. BrSRK-325b and BrSCR-325 were expressed normally at the transcriptional level. The multiple sequence alignment of SCRs and SRKs in class II S haplotypes showed that a number of amino acid variations were present in the contact regions (CR II and CR III) of BrSCR-325 and the hypervariable regions (HV I and HV II) of BrSRK-325s, which may influence the binding and interaction between the ligand and the receptor. Thus, these results suggested that amino acid variations in contact sites may lead to the SI destruction of a new class II S haplotype BrS-325 in B. rapa. The complete SC phenotype of '325' showed the potential for practical breeding application value in B. rapa.
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Affiliation(s)
- Bing Li
- National Sub-Center of Rapeseed Improvement in Wuhan, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (B.L.); (L.W.); (X.L.); (S.D.); (J.T.); (J.S.); (B.Y.); (J.W.); (T.F.); (C.D.)
| | - Xueli Zhang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430345, China; (X.Z.); (L.S.)
| | - Zhiquan Liu
- Hunan Vegetable Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China;
| | - Lulin Wang
- National Sub-Center of Rapeseed Improvement in Wuhan, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (B.L.); (L.W.); (X.L.); (S.D.); (J.T.); (J.S.); (B.Y.); (J.W.); (T.F.); (C.D.)
| | - Liping Song
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430345, China; (X.Z.); (L.S.)
| | - Xiaomei Liang
- National Sub-Center of Rapeseed Improvement in Wuhan, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (B.L.); (L.W.); (X.L.); (S.D.); (J.T.); (J.S.); (B.Y.); (J.W.); (T.F.); (C.D.)
| | - Shengwei Dou
- National Sub-Center of Rapeseed Improvement in Wuhan, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (B.L.); (L.W.); (X.L.); (S.D.); (J.T.); (J.S.); (B.Y.); (J.W.); (T.F.); (C.D.)
| | - Jinxing Tu
- National Sub-Center of Rapeseed Improvement in Wuhan, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (B.L.); (L.W.); (X.L.); (S.D.); (J.T.); (J.S.); (B.Y.); (J.W.); (T.F.); (C.D.)
| | - Jinxiong Shen
- National Sub-Center of Rapeseed Improvement in Wuhan, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (B.L.); (L.W.); (X.L.); (S.D.); (J.T.); (J.S.); (B.Y.); (J.W.); (T.F.); (C.D.)
| | - Bin Yi
- National Sub-Center of Rapeseed Improvement in Wuhan, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (B.L.); (L.W.); (X.L.); (S.D.); (J.T.); (J.S.); (B.Y.); (J.W.); (T.F.); (C.D.)
| | - Jing Wen
- National Sub-Center of Rapeseed Improvement in Wuhan, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (B.L.); (L.W.); (X.L.); (S.D.); (J.T.); (J.S.); (B.Y.); (J.W.); (T.F.); (C.D.)
| | - Tingdong Fu
- National Sub-Center of Rapeseed Improvement in Wuhan, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (B.L.); (L.W.); (X.L.); (S.D.); (J.T.); (J.S.); (B.Y.); (J.W.); (T.F.); (C.D.)
| | - Cheng Dai
- National Sub-Center of Rapeseed Improvement in Wuhan, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (B.L.); (L.W.); (X.L.); (S.D.); (J.T.); (J.S.); (B.Y.); (J.W.); (T.F.); (C.D.)
| | - Changbin Gao
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430345, China; (X.Z.); (L.S.)
- Correspondence: (C.G.); (A.W.); (C.M.); Tel.: +86-27-8728-18-07 (C.M.)
| | - Aihua Wang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430345, China; (X.Z.); (L.S.)
- Correspondence: (C.G.); (A.W.); (C.M.); Tel.: +86-27-8728-18-07 (C.M.)
| | - Chaozhi Ma
- National Sub-Center of Rapeseed Improvement in Wuhan, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (B.L.); (L.W.); (X.L.); (S.D.); (J.T.); (J.S.); (B.Y.); (J.W.); (T.F.); (C.D.)
- Correspondence: (C.G.); (A.W.); (C.M.); Tel.: +86-27-8728-18-07 (C.M.)
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10
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An G, Chen J. Frequent gain- and loss-of-function mutations of the BjMYB113 gene accounted for leaf color variation in Brassica juncea. BMC PLANT BIOLOGY 2021; 21:301. [PMID: 34187365 PMCID: PMC8240407 DOI: 10.1186/s12870-021-03084-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/04/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Mustard (Brassica juncea) is an important economic vegetable, and some cultivars have purple leaves and accumulate more anthocyanins than the green. The genetic and evolution of purple trait in mustard has not been well studied. RESULT In this study, free-hand sections and metabolomics showed that the purple leaves of mustard accumulated more anthocyanins than green ones. The gene controlling purple leaves in mustard, Mustard Purple Leaves (MPL), was genetically mapped and a MYB113-like homolog was identified as the candidate gene. We identified three alleles of the MYB113-like gene, BjMYB113a from a purple cultivar, BjMYB113b and BjMYB113c from green cultivars. A total of 45 single nucleotide polymorphisms (SNPs) and 8 InDels were found between the promoter sequences of the purple allele BjMYB113a and the green allele BjMYB113b. On the other hand, the only sequence variation between the purple allele BjMYB113a and the green allele BjMYB113c is an insertion of 1,033-bp fragment in the 3'region of BjMYB113c. Transgenic assay and promoter activity studies showed that the polymorphism in the promoter region was responsible for the up-regulation of the purple allele BjMYB113a and high accumulation of anthocyanin in the purple cultivar. The up-regulation of BjMYB113a increased the expression of genes in the anthocyanin biosynthesis pathway including BjCHS, BjF3H, BjF3'H, BjDFR, BjANS and BjUGFT, and consequently led to high accumulation of anthocyanin. However, the up-regulation of BjMYB113 was compromised by the insertion of 1,033-bp in 3'region of the allele BjMYB113c. CONCLUSIONS Our results contribute to a better understanding of the genetics and evolution of the BjMYB113 gene controlling purple leaves and provide useful information for further breeding programs of mustard.
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Affiliation(s)
- Guanghui An
- Key Laboratory of Horticultural 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, 430070, Wuhan, People's Republic of China
| | - Jiongjiong Chen
- Key Laboratory of Horticultural 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, 430070, Wuhan, People's Republic of China.
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11
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Yamuangmorn S, Prom-u-Thai C. The Potential of High-Anthocyanin Purple Rice as a Functional Ingredient in Human Health. Antioxidants (Basel) 2021; 10:833. [PMID: 34073767 PMCID: PMC8225073 DOI: 10.3390/antiox10060833] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022] Open
Abstract
Purple rice is recognized as a source of natural anthocyanin compounds among health-conscious consumers who employ rice as their staple food. Anthocyanin is one of the major antioxidant compounds that protect against the reactive oxygen species (ROS) that cause cellular damage in plants and animals, including humans. The physiological role of anthocyanin in plants is not fully understood, but the benefits to human health are apparent against both chronic and non-chronic diseases. This review focuses on anthocyanin synthesis and accumulation in the whole plant of purple rice, from cultivation to the processed end products. The anthocyanin content in purple rice varies due to many factors, including genotype, cultivation, and management as well as post-harvest processing. The cultivation method strongly influences anthocyanin content in rice plants; water conditions, light quantity and quality, and available nutrients in the soil are important factors, while the low stability of anthocyanins means that they can be dramatically degraded under high-temperature conditions. The application of purple rice anthocyanins has been developed in both functional food and other purposes. To maximize the benefits of purple rice to human health, understanding the factors influencing anthocyanin synthesis and accumulation during the entire process from cultivation to product development can be a path for success.
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Affiliation(s)
| | - Chanakan Prom-u-Thai
- Lanna Rice Research Center, Chiang Mai University, Chiang Mai 50200, Thailand;
- Agronomy Division, Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
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12
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Recent Insights into Anthocyanin Pigmentation, Synthesis, Trafficking, and Regulatory Mechanisms in Rice ( Oryza sativa L.) Caryopsis. Biomolecules 2021; 11:biom11030394. [PMID: 33800105 PMCID: PMC8001509 DOI: 10.3390/biom11030394] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/06/2021] [Accepted: 03/01/2021] [Indexed: 01/11/2023] Open
Abstract
Anthocyanins are antioxidants used as natural colorants and are beneficial to human health. Anthocyanins contribute to reactive oxygen species detoxification and sustain plant growth and development under different environmental stresses. They are phenolic compounds that are broadly distributed in nature and are responsible for a wide range of attractive coloration in many plant organs. Anthocyanins are found in various parts of plants such as flowers, leaves, stems, shoots, and grains. Considering their nutritional and health attributes, anthocyanin-enriched rice or pigmented rice cultivars are a possible alternative to reduce malnutrition around the globe. Anthocyanin biosynthesis and storage in rice are complex processes in which several structural and regulatory genes are involved. In recent years, significant progress has been achieved in the molecular and genetic mechanism of anthocyanins, and their synthesis is of great interest to researchers and the scientific community. However, limited studies have reported anthocyanin synthesis, transportation, and environmental conditions that can hinder anthocyanin production in rice. Rice is a staple food around the globe, and further research on anthocyanin in rice warrants more attention. In this review, metabolic and pre-biotic activities, the underlying transportation, and storage mechanisms of anthocyanins in rice are discussed in detail. This review provides potential information for the food industry and clues for rice breeding and genetic engineering of rice.
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13
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Lin M, Sun S, Fang J, Qi X, Sun L, Zhong Y, Sun Y, Hong G, Wang R, Li Y. BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations. BMC Genomics 2021; 22:72. [PMID: 33482717 PMCID: PMC7821520 DOI: 10.1186/s12864-021-07369-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 01/05/2021] [Indexed: 01/02/2023] Open
Abstract
Background Freezing injury, which is an important abiotic stress in horticultural crops, influences the growth and development and the production area of kiwifruit (Actinidia Lind1). Among Actinidia species, Actinidia arguta has excellent cold resistance, but knowledge relevant to molecular mechanisms is still limited. Understanding the mechanism underlying cold resistance in kiwifruit is important for breeding cold resistance. Results In our study, a population resulting from the cross of A. arguta ‘Ruby-3’ × ‘Kuilv’ male was generated for kiwifruit hardiness study, and 20 cold-tolerant and 20 cold-sensitive populations were selected from 492 populations according to their LT50. Then, we performed bulked segregant RNA-seq combined with single-molecule real-time sequencing to identify differentially expressed genes that provide cold hardiness. We found that the content of soluble sucrose and the activity of β-amylase were higher in the cold-tolerant population than in the cold-sensitive population. Upon − 30 °C low-temperature treatment, 126 differentially expressed genes were identify; the expression of 59 genes was up-regulated and that of 67 genes was down-regulated between the tolerant and sensitive pools, respectively. KEGG pathway analysis showed that the DEGs were primarily related to starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism. Ten major key enzyme-encoding genes and two regulatory genes were up-regulated in the tolerant pool, and regulatory genes of the CBF pathway were found to be differentially expressed. In particular, a 14–3-3 gene was down-regulated and an EBF gene was up-regulated. To validate the BSR-Seq results, 24 DEGs were assessed via qRT-PCR, and the results were consistent with those obtained by BSR-Seq. Conclusion Our research provides valuable insights into the mechanism related to cold resistance in Actinidia and identified potential genes that are important for cold resistance in kiwifruit. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07369-9.
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Affiliation(s)
- Miaomiao Lin
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Shihang Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Jinbao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China.
| | - Xiujuan Qi
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China.
| | - Leiming Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Yunpeng Zhong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Yanxiang Sun
- Langfang Normal University, Langfang, 065000, China
| | - Gu Hong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Ran Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Yukuo Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
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14
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Guo Z, Cai L, Chen Z, Wang R, Zhang L, Guan S, Zhang S, Ma W, Liu C, Pan G. Identification of candidate genes controlling chilling tolerance of rice in the cold region at the booting stage by BSA-Seq and RNA-Seq. ROYAL SOCIETY OPEN SCIENCE 2020; 7:201081. [PMID: 33391797 PMCID: PMC7735347 DOI: 10.1098/rsos.201081] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/14/2020] [Indexed: 06/12/2023]
Abstract
Rice is sensitive to low temperatures, specifically at the booting stage. Chilling tolerance of rice is a quantitative trait loci that is governed by multiple genes, and thus, its precise identification through the conventional methods is an arduous task. In this study, we investigated the candidate genes related to chilling tolerance at the booting stage of rice. The F2 population was derived from Longjing25 (chilling-tolerant) and Longjing11 (chilling-sensitive) cross. Two bulked segregant analysis pools were constructed. A 0.82 Mb region containing 98 annotated genes on chromosomes 6 and 9 was recognized as the candidate region associated with chilling tolerance of rice at the booting stage. Transcriptomic analysis of Longjing25 and Longjing11 revealed 50 differentially expressed genes (DEGs) on the candidate intervals. KEGG pathway enrichment analysis of DEGs was performed. Nine pathways were found to be enriched, which contained 10 DEGs. A total of four genes had different expression patterns or levels between Longjing25 and Longjing11. Four out of the 10 DEGs were considered as potential candidate genes for chilling tolerance. This study will assist in the cloning of the candidate genes responsible for chilling tolerance and molecular breeding of rice for the development of chilling-tolerant rice varieties.
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Affiliation(s)
- Zhenhua Guo
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Lijun Cai
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154007, People's Republic of China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Ruiying Wang
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
| | - Lanming Zhang
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
| | - Shiwu Guan
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
| | - Shuhua Zhang
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
| | - Wendong Ma
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
| | - Chuanxue Liu
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
| | - Guojun Pan
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
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15
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Liang T, Chi W, Huang L, Qu M, Zhang S, Chen ZQ, Chen ZJ, Tian D, Gui Y, Chen X, Wang Z, Tang W, Chen S. Bulked Segregant Analysis Coupled with Whole-Genome Sequencing (BSA-Seq) Mapping Identifies a Novel pi21 Haplotype Conferring Basal Resistance to Rice Blast Disease. Int J Mol Sci 2020; 21:ijms21062162. [PMID: 32245192 PMCID: PMC7139700 DOI: 10.3390/ijms21062162] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 01/30/2023] Open
Abstract
Basal or partial resistance has been considered race-non-specific and broad-spectrum. Therefore, the identification of genes or quantitative trait loci (QTLs) conferring basal resistance and germplasm containing them is of significance in breeding crops with durable resistance. In this study, we performed a bulked segregant analysis coupled with whole-genome sequencing (BSA-seq) to identify QTLs controlling basal resistance to blast disease in an F2 population derived from two rice varieties, 02428 and LiXinGeng (LXG), which differ significantly in basal resistance to rice blast. Four candidate QTLs, qBBR-4, qBBR-7, qBBR-8, and qBBR-11, were mapped on chromosomes 4, 7, 8, and 11, respectively. Allelic and genotypic association analyses identified a novel haplotype of the durable blast resistance gene pi21 carrying double deletions of 30 bp and 33 bp in 02428 (pi21-2428) as a candidate gene of qBBR-4. We further assessed haplotypes of Pi21 in 325 rice accessions, and identified 11 haplotypes among the accessions, of which eight were novel types. While the resistant pi21 gene was found only in japonica before, three Chinese indica varieties, ShuHui881, Yong4, and ZhengDa4Hao, were detected carrying the resistant pi21-2428 allele. The pi21-2428 allele and pi21-2428-containing rice germplasm, thus, provide valuable resources for breeding rice varieties, especially indica rice varieties, with durable resistance to blast disease. Our results also lay the foundation for further identification and functional characterization of the other three QTLs to better understand the molecular mechanisms underlying rice basal resistance to blast disease.
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Affiliation(s)
- Tingmin Liang
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou 350108, China; (T.L.); (W.C.); (X.C.); (Z.W.)
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China; (Z.-Q.C.); (Z.-J.C.); (D.T.); (Y.G.)
| | - Wenchao Chi
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou 350108, China; (T.L.); (W.C.); (X.C.); (Z.W.)
| | - Likun Huang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.H.); (S.Z.)
| | - Mengyu Qu
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou 350108, China; (T.L.); (W.C.); (X.C.); (Z.W.)
| | - Shubiao Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.H.); (S.Z.)
| | - Zi-Qiang Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China; (Z.-Q.C.); (Z.-J.C.); (D.T.); (Y.G.)
| | - Zai-Jie Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China; (Z.-Q.C.); (Z.-J.C.); (D.T.); (Y.G.)
| | - Dagang Tian
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China; (Z.-Q.C.); (Z.-J.C.); (D.T.); (Y.G.)
| | - Yijie Gui
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China; (Z.-Q.C.); (Z.-J.C.); (D.T.); (Y.G.)
| | - Xiaofeng Chen
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou 350108, China; (T.L.); (W.C.); (X.C.); (Z.W.)
| | - Zonghua Wang
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou 350108, China; (T.L.); (W.C.); (X.C.); (Z.W.)
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiqi Tang
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou 350108, China; (T.L.); (W.C.); (X.C.); (Z.W.)
- Correspondence: (W.T.); (S.C.)
| | - Songbiao Chen
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou 350108, China; (T.L.); (W.C.); (X.C.); (Z.W.)
- Correspondence: (W.T.); (S.C.)
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