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Zhang L, Fu J, Dong T, Zhang M, Wu J, Liu C. Promoter cloning and activities analysis of JmLFY, a key gene for flowering in Juglans mandshurica. FRONTIERS IN PLANT SCIENCE 2023; 14:1243030. [PMID: 37900747 PMCID: PMC10602732 DOI: 10.3389/fpls.2023.1243030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023]
Abstract
Juglans mandshurica (Manchurian walnut) is a precious timber and woody grain and oil species in Northeast China. The heterodichogamous characteristic phenomenon resulted in the non-synchronous flowering and development of male and female flowers, which limited the mating and the yield and quality of fruits. LFY is a core gene in the flowering regulatory networks, which has been cloned in J. mandshurica, and the function has also been verified preliminarily. In this study, the JmLFY promoter sequence with different lengths of 5'-deletion (pLFY1-pLFY6) were cloned and conducted bioinformatics analysis, the promoter activities were analyzed by detecting their driving activity to GUS gene in the tobacco plants that transformed with different promoter sequence stably or transiently. After that, the interaction between JmSOC1 and JmLFY gene promoter was also analyzed via yeast single-hybrid. The results showed that the promoter sequence contains core cis-acting elements essential for eukaryotic promoters, hormone response elements, defense- and stress-responsive elements, flowering-related elements, etc. Transgenic tobacco plants with pLFY1 were obtained by Agrobacterium infection using the pCAMBIA1301 expression vector, and the GUS gene driven by the JmLFY promoter was detected to express in the leaf, stem, flower, and root of the transformed tobacco plant, which indicated that the obtained JmLFY promoter had driving activity. GUS histochemical staining and enzyme activity detection showed that promoter fragments with different lengths had promoter activity and could respond to the induction of long photoperiod, low temperature, salicylic acid (SA), IAA, GA3, and methyl jasmonate (MeJA). The core regulatory region of JmLFY gene promoter in J. mandshurica was between -657 bp and -1,904 bp. Point-to-point validation of yeast single-hybrid confirmed the interaction between JmSOC1 and JmLFY gene promoter, which indicated that JmLFY gene is the downstream target of JmSOC1. These results reveal relevant factors affecting JmLFY gene expression and clarify the molecular mechanism of JmLFY gene regulation in the flower developmental partially, which will provide a theoretical basis for regulating the flowering time by regulating JmLFY gene expression in J. mandshurica.
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Affiliation(s)
- Lijie Zhang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Jingqi Fu
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Tianyi Dong
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Mengmeng Zhang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Jingwen Wu
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Chunping Liu
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Silviculture of Liaoning Province , Shenyang, China
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Wang J, Zhang B, Guo H, Chen L, Han F, Yan C, Yang L, Zhuang M, Lv H, Wang Y, Ji J, Zhang Y. Transcriptome Analysis Reveals Key Genes and Pathways Associated with the Regulation of Flowering Time in Cabbage ( Brassica oleracea L. var. capitata). PLANTS (BASEL, SWITZERLAND) 2023; 12:3413. [PMID: 37836153 PMCID: PMC10574337 DOI: 10.3390/plants12193413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/17/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023]
Abstract
Flowering time is an important agronomic trait in cabbage (Brassica oleracea L. var. capitata), but the molecular regulatory mechanism underlying flowering time regulation in cabbage remains unclear. In this study, transcriptome analysis was performed using two sets of cabbage materials: (1) the early-flowering inbred line C491 (P1) and late-flowering inbred line B602 (P2), (2) the early-flowering individuals F2-B and late-flowering individuals F2-NB from the F2 population. The analysis revealed 9508 differentially expressed genes (DEGs) common to both C491_VS_ B602 and F2-B_VS_F2-NB. The Kyoto Encyclopedia of Genes and Genomes (KEGGs) analysis showed that plant hormone signal transduction and the MAPK signaling pathway were mainly enriched in up-regulated genes, and ribosome and DNA replication were mainly enriched in down-regulated genes. We identified 321 homologues of Arabidopsis flowering time genes (Ft) in cabbage. Among them, 25 DEGs (11 up-regulated and 14 down-regulated genes) were detected in the two comparison groups, and 12 gene expression patterns closely corresponded with the different flowering times in the two sets of materials. Two genes encoding MADS-box proteins, Bo1g157450 (BoSEP2-1) and Bo5g152700 (BoSEP2-2), showed significantly reduced expression in the late-flowering parent B602 compared with the early-flowering parent C491 via qRT-PCR analysis, which was consistent with the RNA-seq data. Next, the expression levels of Bo1g157450 (BoSEP2-1) and Bo5g152700 (BoSEP2-2) were analyzed in two other groups of early-flowering and late-flowering inbred lines, which showed that their expression patterns were consistent with those in the parents. Sequence analysis revealed that three and one SNPs between B602 and C491 were identified in Bo1g157450 (BoSEP2-1) and Bo5g152700 (BoSEP2-2), respectively. Therefore, BoSEP2-1 and BoSEP2-2 were designated as candidates for flowering time regulation through a potential new regulatory pathway. These results provide new insights into the molecular mechanisms underlying flowering time regulation in cabbage.
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Affiliation(s)
- Jiao Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China;
| | - Bin Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Huiling Guo
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Li Chen
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Fengqing Han
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Chao Yan
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China;
| | - Limei Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Mu Zhuang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Honghao Lv
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Yong Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Jialei Ji
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Yangyong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
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Liu Q, Wang Y, Fu Y, Du L, Zhang Y, Wang Q, Sun R, Ai N, Feng G, Li C. Genetic dissection of lint percentage in short-season cotton using combined QTL mapping and RNA-seq. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:205. [PMID: 37668671 DOI: 10.1007/s00122-023-04453-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023]
Abstract
KEY MESSAGE In total, 17 QTLs for lint percentage in short-season cotton, including three stable QTLs, were detected. Twenty-eight differentially expressed genes located within the stable QTLs were identified, and two genes were validated by qRT-PCR. The breeding and use of short-season cotton have significant values in addressing the question of occupying farmlands with either cotton or cereals. However, the fiber yields of short-season cotton varieties are significantly lower than those of middle- and late-maturing varieties. How to effectively improve the fiber yield of short-season cotton has become a focus of cotton research. Here, a high-density genetic map was constructed using genome resequencing and an RIL population generated from the hybridization of two short-season cotton accessions, Dong3 and Dong4. The map contained 4960 bin markers across the 26 cotton chromosomes and spanned 3971.08 cM, with an average distance of 0.80 cM between adjacent markers. Based on the genetic map, quantitative trait locus (QTL) mapping for lint percentage (LP, %), an important yield component trait, was performed. In total, 17 QTLs for LP, including three stable QTLs, qLP-A02, qLP-D04, and qLP-D12, were detected. Three out of 11 non-redundant QTLs overlapped with previously reported QTLs, whereas the other eight were novel QTLs. A total of 28 differentially expressed genes associated with the three stable QTLs were identified using RNA-seq of ovules and fibers at different seed developmental stages from the parental materials. The two genes, Ghir_A02G017640 and Ghir_A02G018500, may be related to LP as determined by further qRT-PCR validation. This study provides useful information for the genetic dissection of LP and promotes the molecular breeding of short-season cotton.
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Affiliation(s)
- Qiao Liu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yuanyuan Wang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yuanzhi Fu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Lei Du
- Life Science College, Yuncheng University, Yuncheng, 044000, China
| | - Yilin Zhang
- Life Science College, Yuncheng University, Yuncheng, 044000, China
| | - Qinglian Wang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Runrun Sun
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Nijiang Ai
- Shihezi Academy of Agricultural Sciences, Shihezi, 832000, China
| | - Guoli Feng
- Shihezi Academy of Agricultural Sciences, Shihezi, 832000, China
| | - Chengqi Li
- Life Science College, Yuncheng University, Yuncheng, 044000, China.
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Starosta E, Szwarc J, Niemann J, Szewczyk K, Weigt D. Brassica napus Haploid and Double Haploid Production and Its Latest Applications. Curr Issues Mol Biol 2023; 45:4431-4450. [PMID: 37232751 DOI: 10.3390/cimb45050282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/05/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
Rapeseed is one of the most important oil crops in the world. Increasing demand for oil and limited agronomic capabilities of present-day rapeseed result in the need for rapid development of new, superior cultivars. Double haploid (DH) technology is a fast and convenient approach in plant breeding as well as genetic research. Brassica napus is considered a model species for DH production based on microspore embryogenesis; however, the molecular mechanisms underlying microspore reprogramming are still vague. It is known that morphological changes are accompanied by gene and protein expression patterns, alongside carbohydrate and lipid metabolism. Novel, more efficient methods for DH rapeseed production have been reported. This review covers new findings and advances in Brassica napus DH production as well as the latest reports related to agronomically important traits in molecular studies employing the double haploid rapeseed lines.
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Affiliation(s)
- Ewa Starosta
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Justyna Szwarc
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Janetta Niemann
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Katarzyna Szewczyk
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Dorota Weigt
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
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Zhang Y, Zhang Q, Wang H, Tao S, Cao H, Shi Y, Bakirov A, Xu A, Huang Z. Discovery of common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits in Brassica napus L. PLANT CELL REPORTS 2023; 42:1039-1057. [PMID: 37076701 DOI: 10.1007/s00299-023-03011-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits were identified in Brassica napus combining QTL mapping with transcriptome under salt and alkaline stresses. The yield of rapeseed (Brassica napus L.) is determined by multiple yield-related traits, which are susceptible to environmental factors. Many yield-related quantitative trait loci (QTLs) have been reported in Brassica napus; however, no studies have been conducted to investigate both salt-alkali tolerance and yield-related traits simultaneously. Here, specific-locus amplified fragment sequencing (SLAF-seq) technologies were utilized to map the QTLs for salt-alkali tolerance and yield-related traits. A total of 65 QTLs were identified, including 30 QTLs for salt-alkali tolerance traits and 35 QTLs for yield-related traits, accounting for 7.61-27.84% of the total phenotypic variations. Among these QTLs, 18 unique QTLs controlling two to four traits were identified by meta-analysis. Six novel and unique QTLs were detected for salt-alkali tolerance traits. By comparing these unique QTLs for salt-alkali tolerance traits with those previously reported QTLs for yield-related traits, seven co-localized chromosomal regions were identified on A09 and A10. Combining QTL mapping with transcriptome of two parents under salt and alkaline stresses, thirteen genes were identified as the candidates controlling both salt-alkali tolerance and yield. These findings provide useful information for future breeding of high-yield cultivars resistant to alkaline and salt stresses.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qi Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Han Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shunxian Tao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hanming Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yiji Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Aldiyar Bakirov
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Aixia Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Orantes-Bonilla M, Wang H, Lee HT, Golicz AA, Hu D, Li W, Zou J, Snowdon RJ. Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:113. [PMID: 37071201 PMCID: PMC10113308 DOI: 10.1007/s00122-023-04345-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/12/2023] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE Transcriptomic and epigenomic profiling of gene expression and small RNAs during seed and seedling development reveals expression and methylation dominance levels with implications on early stage heterosis in oilseed rape. The enhanced performance of hybrids through heterosis remains a key aspect in plant breeding; however, the underlying mechanisms are still not fully elucidated. To investigate the potential role of transcriptomic and epigenomic patterns in early expression of hybrid vigor, we investigated gene expression, small RNA abundance and genome-wide methylation in hybrids from two distant Brassica napus ecotypes during seed and seedling developmental stages using next-generation sequencing. A total of 31117, 344, 36229 and 7399 differentially expressed genes, microRNAs, small interfering RNAs and differentially methylated regions were identified, respectively. Approximately 70% of the differentially expressed or methylated features displayed parental dominance levels where the hybrid followed the same patterns as the parents. Via gene ontology enrichment and microRNA-target association analyses during seed development, we found copies of reproductive, developmental and meiotic genes with transgressive and paternal dominance patterns. Interestingly, maternal dominance was more prominent in hypermethylated and downregulated features during seed formation, contrasting to the general maternal gamete demethylation reported during gametogenesis in angiosperms. Associations between methylation and gene expression allowed identification of putative epialleles with diverse pivotal biological functions during seed formation. Furthermore, most differentially methylated regions, differentially expressed siRNAs and transposable elements were in regions that flanked genes without differential expression. This suggests that differential expression and methylation of epigenomic features may help maintain expression of pivotal genes in a hybrid context. Differential expression and methylation patterns during seed formation in an F1 hybrid provide novel insights into genes and mechanisms with potential roles in early heterosis.
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Affiliation(s)
- Mauricio Orantes-Bonilla
- Department of Plant Breeding, Land Use and Nutrition, IFZ Research Centre for Biosystems, Justus Liebig University, Giessen, Germany
| | - Hao Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Huey Tyng Lee
- Department of Plant Breeding, Land Use and Nutrition, IFZ Research Centre for Biosystems, Justus Liebig University, Giessen, Germany
| | - Agnieszka A Golicz
- Department of Plant Breeding, Land Use and Nutrition, IFZ Research Centre for Biosystems, Justus Liebig University, Giessen, Germany
| | - Dandan Hu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Wenwen Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Rod J Snowdon
- Department of Plant Breeding, Land Use and Nutrition, IFZ Research Centre for Biosystems, Justus Liebig University, Giessen, Germany.
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Xu Y, Kong X, Guo Y, Wang R, Yao X, Chen X, Yan T, Wu D, Lu Y, Dong J, Zhu Y, Chen M, Cen H, Jiang L. Structural variations and environmental specificities of flowering time-related genes in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:42. [PMID: 36897406 DOI: 10.1007/s00122-023-04326-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
We found that the flowering time order of accessions in a genetic population considerably varied across environments, and homolog copies of essential flowering time genes played different roles in different locations. Flowering time plays a critical role in determining the life cycle length, yield, and quality of a crop. However, the allelic polymorphism of flowering time-related genes (FTRGs) in Brassica napus, an important oil crop, remains unclear. Here, we provide high-resolution graphics of FTRGs in B. napus on a pangenome-wide scale based on single nucleotide polymorphism (SNP) and structural variation (SV) analyses. A total of 1337 FTRGs in B. napus were identified by aligning their coding sequences with Arabidopsis orthologs. Overall, 46.07% of FTRGs were core genes and 53.93% were variable genes. Moreover, 1.94%, 0.74%, and 4.49% FTRGs had significant presence-frequency differences (PFDs) between the spring and semi-winter, spring and winter, and winter and semi-winter ecotypes, respectively. SNPs and SVs across 1626 accessions of 39 FTRGs underlying numerous published qualitative trait loci were analyzed. Additionally, to identify FTRGs specific to an eco-condition, genome-wide association studies (GWASs) based on SNP, presence/absence variation (PAV), and SV were performed after growing and observing the flowering time order (FTO) of plants in a collection of 292 accessions at three locations in two successive years. It was discovered that the FTO of plants in a genetic population changed a lot across various environments, and homolog copies of some key FTRGs played different roles in different locations. This study revealed the molecular basis of the genotype-by-environment (G × E) effect on flowering and recommended a pool of candidate genes specific to locations for breeding selection.
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Affiliation(s)
- Ying Xu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Xiangdong Kong
- Jiguang Gene Biotechnology Co., Ltd., Nanjing, 210000, China
| | - Yuan Guo
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Ruisen Wang
- Jiaxing Academy of Agricultural Sciences, Jiaxing, 31400, China
| | - Xiangtan Yao
- Jiaxing Academy of Agricultural Sciences, Jiaxing, 31400, China
| | - Xiaoyang Chen
- Jinhua Academy of Agricultural Sciences, Jinhua, 321017, China
| | - Tao Yan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Dezhi Wu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Yunhai Lu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Jie Dong
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Yang Zhu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Mingxun Chen
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Haiyan Cen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
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Cai J, Jia R, Jiang Y, Fu J, Dong T, Deng J, Zhang L. Functional verification of the JmLFY gene associated with the flowering of Juglans mandshurica Maxim. PeerJ 2023; 11:e14938. [PMID: 36908820 PMCID: PMC10000305 DOI: 10.7717/peerj.14938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/31/2023] [Indexed: 03/09/2023] Open
Abstract
In this study, a pBI121-JmLFY plant expression vector was constructed on the basis of obtaining the full-length sequence of the JmLFY gene from Juglans mandshurica, which was then used for genetic transformation via Agrobacterium inflorescence infection using wild-type Arabidopsis thaliana and lfy mutants as transgenic receptors. Seeds of positive A. thaliana plants with high expression of JmLFY were collected and sowed till the homozygous T3 regeneration plants were obtained. Then the expression of flowering-related genes (AtAP1, AtSOC1, AtFT and AtPI) in T3 generation plants were analyzed and the results showed that JmLFY gene overexpression promoted the expression of flowering-related genes and resulted in earlier flowering in A. thaliana. The A. thaliana plants of JmLFY-transformed and JmLFY-transformed lfy mutants appeared shorter leaves, longer fruit pods, and fewer cauline leaves than those of wild-type and the lfy mutants plants, respectively. In addition, some secondary branches in the transgenic plants converted into inflorescences, which indicated that the overexpression of JmLFY promoted the transition from vegetative growth to reproductive growth, and compensate the phenotypic defects of lfy mutant partially. The results provides a scientific reference for formulating reasonable genetic improvement strategies such as shortening childhood, improving yield and quality, and breeding desirable varieties, which have important guiding significance in production.
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Affiliation(s)
- Jiayou Cai
- Shenyang Agricultural University, Shenyang, Liaoning, China
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang, Liaoning, China
| | - Ruoxue Jia
- Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Ying Jiang
- Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Jingqi Fu
- Shenyang Agricultural University, Shenyang, Liaoning, China
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang, Liaoning, China
| | - Tianyi Dong
- Shenyang Agricultural University, Shenyang, Liaoning, China
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang, Liaoning, China
| | - Jifeng Deng
- Shenyang Agricultural University, Shenyang, Liaoning, China
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang, Liaoning, China
| | - Lijie Zhang
- Shenyang Agricultural University, Shenyang, Liaoning, China
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang, Liaoning, China
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Gill RA, Helal MMU, Tang M, Hu M, Tong C, Liu S. High-Throughput Association Mapping in Brassica napus L.: Methods and Applications. Methods Mol Biol 2023; 2638:67-91. [PMID: 36781636 DOI: 10.1007/978-1-0716-3024-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Oil seed rape (Braasica napus L.) is ranked second among oil seed crops cultivated globally for edible oil for human, and seed cake for animal consumption. Recent genetic and genomics advancements highlighted the diversity that exists within B. napus, which is largely discovered using the most promising genetic markers called single nucleotide polymorphism (SNP). Their calling rate is also enhanced to ~100 folds after the continuous advancements in the next generation sequencing (NGS) technologies. As the high throughput of NGS resulted in multi-Giga bases data, the detailed quality control (QC) prior to downstream analyses is a pre-requisite. It mainly involved the removal of false positives, missing proportions, filtering of low-quality SNPs, and adjustments of minor-allele frequency and heterozygosity. After marker-trait association, for conformation of target SNPs, validations of SNPs can be performed using various methods, especially allele-specific PCR assay-based methods have been utilized for SNP genotyping of genes targeting agronomic traits and somaclonal variations occurred during transgenic studies. In the present study, the authors mainly argue on the genotypic progress, and pipelines/methods that are being used for detection, calling, filtering, and validation of SNPs. Also, insight is provided into the application of SNPs in linkage and association mapping, including QTL mapping and genome-wide association studies targeting mainly developmental traits related to the root system and plant architecture, flowering time, silique, and oil quality. Briefly, the present study provides the recent information and recommendations on the SNP genotyping methods and its applications, which can be useful for marker-assisted breeding in B. napus and other crops.
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Affiliation(s)
- Rafaqat Ali Gill
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Md Mostofa Uddin Helal
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Minqiang Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Ming Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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10
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Benaouda S, Stöcker T, Schoof H, Léon J, Ballvora A. Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat. BMC PLANT BIOLOGY 2023; 23:25. [PMID: 36631761 PMCID: PMC9835304 DOI: 10.1186/s12870-022-03986-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The transition from vegetative to floral phase is the result of complex crosstalk of exogenous and endogenous floral integrators. This critical physiological event is the response to environmental interaction, which causes biochemical cascades of reactions at different internal tissues, organs, and releases signals that make the plant moves from vegetative status to a reproductive phase. This network controlling flowering time is not deciphered largely in bread wheat. In this study, a comparative transcriptome analysis at a transition time in combination with genetic mapping was used to identify responsible genes in a stage and tissue-specific manner. For this reason, two winter cultivars that have been bred in Germany showing contrasting and stable heading time in different environments were selected for the analysis. RESULTS In total, 670 and 1075 differentially expressed genes in the shoot apical meristem and leaf tissue, respectively, could be identified in 23 QTL intervals for the heading date. In the transition apex, Histone methylation H3-K36 and regulation of circadian rhythm are both controlled by the same homoeolog genes mapped in QTL TaHd112, TaHd124, and TaHd137. TaAGL14 gene that identifies the floral meristem was mapped in TaHd054 in the double ridge. In the same stage, the homoeolog located on chromosome 7D of FLOWERING TIME LOCUS T mapped on chr 7B, which evolved an antagonist function and acts as a flowering repressor was uncovered. The wheat orthologue of transcription factor ASYMMETRIC LEAVES 1 (AS1) was identified in the late reproductive stage and was mapped in TaHd102, which is strongly associated with heading date. Deletion of eight nucleotides in the AS1 promoter could be identified in the binding site of the SUPPRESSOR OF CONSTANS OVEREXPRESSION 1 (SOC1) gene in the late flowering cultivar. Both proteins AS1 and SOC1 are inducing flowering time in response to gibberellin biosynthesis. CONCLUSION The global transcriptomic at the transition phase uncovered stage and tissue-specific genes mapped in QTL of heading date in winter wheat. In response to Gibberellin signaling, wheat orthologous transcription factor AS1 is expressed in the late reproductive phase of the floral transition. The locus harboring this gene is the strongest QTL associated with the heading date trait in the German cultivars. Consequently, we conclude that this is another indication of the Gibberellin biosynthesis as the mechanism behind the heading variation in wheat.
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Affiliation(s)
- Salma Benaouda
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Tyll Stöcker
- Institute for Crop Science and Resource Conservation, Chair of Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Heiko Schoof
- Institute for Crop Science and Resource Conservation, Chair of Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Jens Léon
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
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11
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Shen F, Hu C, Huang X, Wu R, Luo S, Xu C, Zhang H, Wang X, Zhao J. Characterization of the genetic and regulatory networks associated with sugar and acid metabolism in apples via an integrated strategy. FRONTIERS IN PLANT SCIENCE 2022; 13:1066592. [PMID: 36466245 PMCID: PMC9712955 DOI: 10.3389/fpls.2022.1066592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Although sugars and acids have a substantial influence on the taste of apple fruits, the genetic and regulatory networks underlying their metabolism in fruit remain insufficiently determined. To fully decipher the genetic basis of the accumulation of sugars and acids in apple fruits, we adopted an integrated strategy that included time-course RNA-seq, QTL mapping, and whole-genome sequencing to examine two typical cultivars ('HanFu' and 'Huahong') characterized by distinctive flavors. Whole-genome sequencing revealed substantial genetic variation between the two cultivars, thereby providing an indication of the genetic basis of the distinct phenotypes. Constructed co-expression networks yielded information regarding the intra-relationships among the accumulation of different types of metabolites, and also revealed key regulatory nodes associated with the accumulation of sugars and acids, including the genes MdEF2, MdPILS5, and MdGUN8. Additionally, on the basis of QTL mapping using a high-density genetic map, we identified a series of QTLs and functional genes underlying vital traits, including sugar and acid contents. Collectively, our methodology and observations will provide an important reference for further studies focusing on the flavor of apples.
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Affiliation(s)
- Fei Shen
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chenyang Hu
- College of Life Science, Shanxi Key Lab of Chinese Jujube, Yan’an University, Yan’an, Shanxi, China
| | - Xin Huang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, Hebei, China
| | - Ruigang Wu
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, Hebei, China
| | - Shuzhen Luo
- College of Life Science, Shanxi Key Lab of Chinese Jujube, Yan’an University, Yan’an, Shanxi, China
| | - Chengnan Xu
- College of Life Science, Shanxi Key Lab of Chinese Jujube, Yan’an University, Yan’an, Shanxi, China
| | - Hong Zhang
- College of Life Science, Shanxi Key Lab of Chinese Jujube, Yan’an University, Yan’an, Shanxi, China
| | - Xuan Wang
- Hebei Normal University of Science & Technology, Qinhuangdao, Hebei, China
| | - Jirong Zhao
- College of Life Science, Shanxi Key Lab of Chinese Jujube, Yan’an University, Yan’an, Shanxi, China
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12
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Chen L, Lei W, He W, Wang Y, Tian J, Gong J, Hao B, Cheng X, Shu Y, Fan Z. Mapping of Two Major QTLs Controlling Flowering Time in Brassica napus Using a High-Density Genetic Map. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11192635. [PMID: 36235500 PMCID: PMC9571212 DOI: 10.3390/plants11192635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/01/2022] [Accepted: 10/05/2022] [Indexed: 05/31/2023]
Abstract
Research on the flowering habit of rapeseed is important for the selection of varieties adapted to specific ecological environments. Here, quantitative trait loci (QTL) for the days-to-flowering trait were identified using a doubled haploid population of 178 lines derived from a cross between the winter type SGDH284 and the semi-winter type 158A. A linkage map encompassing 3268.01 cM was constructed using 2777 bin markers obtained from next-generation sequencing. The preliminary mapping results revealed 56 QTLs for the days to flowering in the six replicates in the three environments. Twelve consensus QTLs were identified by a QTL meta-analysis, two of which (cqDTF-C02 and cqDTF-C06) were designated as major QTLs. Based on the micro-collinearity of the target regions between B. napus and Arabidopsis, four genes possibly related to flowering time were identified in the cqDTF-C02 interval, and only one gene possibly related to flowering time was identified in the cqDTF-C06 interval. A tightly linked insertion-deletion marker for the cqFT-C02 locus was developed. These findings will aid the breeding of early maturing B. napus varieties.
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Affiliation(s)
- Lei Chen
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China
| | - Weixia Lei
- Crop Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Wangfei He
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China
| | - Yifan Wang
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China
| | - Jie Tian
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China
| | - Jihui Gong
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China
| | - Bing Hao
- Bengbu Ludu Crop Residue Biotechnology Co., Ltd., Bengbu 233000, China
| | - Xinxin Cheng
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China
| | - Yingjie Shu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China
| | - Zhixiong Fan
- Crop Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
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13
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Singh KP, Kumari P, Yadava DK. Development of de-novo transcriptome assembly and SSRs in allohexaploid Brassica with functional annotations and identification of heat-shock proteins for thermotolerance. Front Genet 2022; 13:958217. [PMID: 36186472 PMCID: PMC9524822 DOI: 10.3389/fgene.2022.958217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/23/2022] [Indexed: 11/20/2022] Open
Abstract
Crop Brassicas contain monogenomic and digenomic species, with no evidence of a trigenomic Brassica in nature. Through somatic fusion (Sinapis alba + B. juncea), a novel allohexaploid trigenomic Brassica (H1 = AABBSS; 2n = 60) was produced and used for transcriptome analysis to uncover genes for thermotolerance, annotations, and microsatellite markers for future molecular breeding. Illumina Novaseq 6000 generated a total of 76,055,546 paired-end raw reads, which were used for de-novo assembly, resulting in the development of 486,066 transcripts. A total of 133,167 coding sequences (CDSs) were predicted from transcripts with a mean length of 507.12 bp and 46.15% GC content. The BLASTX search of CDSs against public protein databases showed a maximum of 126,131 (94.72%) and a minimum of 29,810 (22.39%) positive hits. Furthermore, 953,773 gene ontology (GO) terms were found in 77,613 (58.28%) CDSs, which were divided into biological processes (49.06%), cellular components (31.67%), and molecular functions (19.27%). CDSs were assigned to 144 pathways by a pathway study using the KEGG database and 1,551 pathways by a similar analysis using the Reactome database. Further investigation led to the discovery of genes encoding over 2,000 heat shock proteins (HSPs). The discovery of a large number of HSPs in allohexaploid Brassica validated our earlier findings for heat tolerance at seed maturity. A total of 15,736 SSRs have been found in 13,595 CDSs, with an average of one SSR per 4.29 kb length and an SSR frequency of 11.82%. The first transcriptome assembly of a meiotically stable allohexaploid Brassica has been given in this article, along with functional annotations and the presence of SSRs, which could aid future genetic and genomic studies.
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Affiliation(s)
| | - Preetesh Kumari
- Genetics Division, ICAR—Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Preetesh Kumari,
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14
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Hill MJ, Penning BW, McCann MC, Carpita NC. COMPILE: a GWAS computational pipeline for gene discovery in complex genomes. BMC PLANT BIOLOGY 2022; 22:315. [PMID: 35778686 PMCID: PMC9250234 DOI: 10.1186/s12870-022-03668-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. RESULTS COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer (Ostrinia nubilalis). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. CONCLUSIONS The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.
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Affiliation(s)
- Matthew J Hill
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
- Present address: Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA
- Present address: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bryan W Penning
- USDA-ARS Corn, Soybean and Wheat Quality Research Unit, Wooster, OH, 44691, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
- Present address: Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA.
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA.
- Present address: Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
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15
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Liu Z, Dong X, Zheng G, Xu C, Wei J, Cui J, Cao X, Li H, Fang X, Wang Y, Tian H. Integrate QTL Mapping and Transcription Profiles Reveal Candidate Genes Regulating Flowering Time in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:904198. [PMID: 35837459 PMCID: PMC9274139 DOI: 10.3389/fpls.2022.904198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Flowering at the proper time is an important part of acclimation to the ambient environment and season and maximizes the plant yield. To reveal the genetic architecture and molecular regulation of flowering time in oilseed rape (Brassica napus), we performed an RNA-seq analysis of the two parents after vernalization at low temperature and combined this with quantitative trait loci (QTL) mapping in an F2 population. A genetic linkage map that included 1,017 markers merged into 268 bins and covered 793.53 cM was constructed. Two QTLs associated with flowering time were detected in the F2 population. qFTA06 was the major QTL in the 7.06 Mb interval on chromosome A06 and accounted for 19.3% of the phenotypic variation. qFTC08 was located on chromosome C06 and accounted for 8.6% of the phenotypic variation. RNA-seq analysis revealed 4,626 differentially expressed genes (DEGs) between two parents during vernalization. Integration between QTL mapping and RNA-seq analysis revealed six candidate genes involved in the regulation of flowering time through the circadian clock/photoperiod, auxin and ABA hormone signal, and cold signal transduction and vernalization pathways. These results provide insights into the molecular genetic architecture of flowering time in B. napus.
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16
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Raboanatahiry N, Chao H, He J, Li H, Yin Y, Li M. Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:862363. [PMID: 35360294 PMCID: PMC8963808 DOI: 10.3389/fpls.2022.862363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/15/2022] [Indexed: 06/12/2023]
Abstract
Rapeseed is the second most important oil crop in the world. Improving seed yield and seed oil content are the two main highlights of the research. Unfortunately, rapeseed development is frequently affected by different diseases. Extensive research has been made through many years to develop elite cultivars with high oil, high yield, and/or disease resistance. Quantitative trait locus (QTL) analysis has been one of the most important strategies in the genetic deciphering of agronomic characteristics. To comprehend the distribution of these QTLs and to uncover the key regions that could simultaneously control multiple traits, 4,555 QTLs that have been identified during the last 25 years were aligned in one unique map, and a quantitative genomic map which involved 128 traits from 79 populations developed in 12 countries was constructed. The present study revealed 517 regions of overlapping QTLs which harbored 2,744 candidate genes and might affect multiple traits, simultaneously. They could be selected to customize super-rapeseed cultivars. The gene ontology and the interaction network of those candidates revealed genes that highly interacted with the other genes and might have a strong influence on them. The expression and structure of these candidate genes were compared in eight rapeseed accessions and revealed genes of similar structures which were expressed differently. The present study enriches our knowledge of rapeseed genome characteristics and diversity, and it also provided indications for rapeseed molecular breeding improvement in the future.
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Affiliation(s)
- Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yongtai Yin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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17
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Yang J, Gao L, Liu X, Zhang X, Wang X, Wang Z. Comparative transcriptome analysis of fiber and nonfiber tissues to identify the genes preferentially expressed in fiber development in Gossypium hirsutum. Sci Rep 2021; 11:22833. [PMID: 34819523 PMCID: PMC8613186 DOI: 10.1038/s41598-021-01829-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 11/02/2021] [Indexed: 02/06/2023] Open
Abstract
Cotton is an important natural fiber crop and economic crop worldwide. The quality of cotton fiber directly determines the quality of cotton textiles. Identifying cotton fiber development-related genes and exploring their biological functions will not only help to better understand the elongation and development mechanisms of cotton fibers but also provide a theoretical basis for the cultivation of new cotton varieties with excellent fiber quality. In this study, RNA sequencing technology was used to construct transcriptome databases for different nonfiber tissues (root, leaf, anther and stigma) and fiber developmental stages (7 days post-anthesis (DPA), 14 DPA, and 26 DPA) of upland cotton Coker 312. The sizes of the seven transcriptome databases constructed ranged from 4.43 to 5.20 Gb, corresponding to approximately twice the genome size of Gossypium hirsutum (2.5 Gb). Among the obtained clean reads, 83.32% to 88.22% could be compared to the upland cotton TM-1 reference genome. By analyzing the differential gene expression profiles of the transcriptome libraries of fiber and nonfiber tissues, we obtained 1205, 1135 and 937 genes with significantly upregulated expression at 7 DPA, 14 DPA and 26 DPA, respectively, and 124, 179 and 213 genes with significantly downregulated expression. Subsequently, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed, which revealed that these genes were mainly involved in catalytic activity, carbohydrate metabolism, the cell membrane and organelles, signal transduction and other functions and metabolic pathways. Through gene annotation analysis, many transcription factors and genes related to fiber development were screened. Thirty-six genes were randomly selected from the significantly upregulated genes in fiber, and expression profile analysis was performed using qRT-PCR. The results were highly consistent with the gene expression profile analyzed by RNA-seq, and all of the genes were specifically or predominantly expressed in fiber. Therefore, our RNA sequencing-based comparative transcriptome analysis will lay a foundation for future research to provide new genetic resources for the genetic engineering of improved cotton fiber quality and for cultivating new transgenic cotton germplasms for fiber quality improvement.
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Affiliation(s)
- Jiangtao Yang
- Biotechnology Research Institute, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lihua Gao
- School of Life Sciences, Langfang Normal University, Langfang, 065000, China
| | - Xiaojing Liu
- Biotechnology Research Institute, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaochun Zhang
- Biotechnology Research Institute, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xujing Wang
- Biotechnology Research Institute, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Zhixing Wang
- Biotechnology Research Institute, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Helal MMU, Gill RA, Tang M, Yang L, Hu M, Yang L, Xie M, Zhao C, Cheng X, Zhang Y, Zhang X, Liu S. SNP- and Haplotype-Based GWAS of Flowering-Related Traits in Brassica napus. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112475. [PMID: 34834840 PMCID: PMC8619824 DOI: 10.3390/plants10112475] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 05/05/2023]
Abstract
Traits related to flowering time are the most promising agronomic traits that directly impact the seed yield and oil quality of rapeseed (Brassica napus L.). Developing early flowering and maturity rapeseed varieties is an important breeding objective in B. napus. Many studies have reported on days to flowering, but few have reported on budding, bolting, and the interval between bolting and DTF. Therefore, elucidating the genetic architecture of QTLs and genes regulating flowering time, we presented an integrated investigation on SNP and haplotype-based genome-wide association study of 373 diverse B. napus germplasm, which were genotyped by the 60K SNP array and were phenotyped in the four environments. The results showed that a total of 15 and 37 QTLs were detected from SNP and haplotype-based GWAS, respectively. Among them, seven QTL clusters were identified by haplotype-based GWAS. Moreover, three and eight environmentally stable QTLs were detected by SNP-GWAS and haplotype-based GWAS, respectively. By integrating the above two approaches and by co-localizing the four traits, ten (10) genomic regions were under selection on chromosomes A03, A07, A08, A10, C06, C07, and C08. Interestingly, the genomic regions FT.A07.1, FT.A08, FT.C06, and FT.C07 were identified as novel. In these ten regions, a total of 197 genes controlling FT were detected, of which 14 highly expressed DEGs were orthologous to 13 Arabidopsis thaliana genes after integration with transcriptome results. In a nutshell, the above results uncovered the genetic architecture of important agronomic traits related to flowering time and provided a basis for multiple molecular marker-trait associations in B. napus.
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Affiliation(s)
- MMU Helal
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Rafaqat Ali Gill
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Minqiang Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
- Key Laboratory of Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), College of Forestry, Hainan University, Haikou 570228, China
| | - Li Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Ming Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Lingli Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Meili Xie
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Chuanji Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Xiaohui Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Yuanyuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
- Correspondence: (Y.Z.); (X.Z.)
| | - Xiong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
- Correspondence: (Y.Z.); (X.Z.)
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
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Song J, Li B, Cui Y, Zhuo C, Gu Y, Hu K, Wen J, Yi B, Shen J, Ma C, Fu T, Tu J. QTL Mapping and Diurnal Transcriptome Analysis Identify Candidate Genes Regulating Brassica napus Flowering Time. Int J Mol Sci 2021; 22:ijms22147559. [PMID: 34299178 PMCID: PMC8305928 DOI: 10.3390/ijms22147559] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/04/2021] [Accepted: 07/07/2021] [Indexed: 12/16/2022] Open
Abstract
Timely flowering is important for seed formation and maximization of rapeseed (Brassica napus) yield. Here, we performed flowering-time quantitative trait loci (QTL) mapping using a double haploid (DH) population grown in three environments to study the genetic architecture. Brassica 60 K Illumina Infinium™ single nucleotide polymorphism (SNP) array and simple sequence repeat (SSR) markers were used for genotyping of the DH population, and a high-density genetic linkage map was constructed. QTL analysis of flowering time from the three environments revealed five consensus QTLs, including two major QTLs. A major QTL located on chromosome A03 was detected specifically in the semi-winter rapeseed growing region, and the one on chromosome C08 was detected in all environments. Ribonucleic acid sequencing (RNA-seq) was performed on the parents’ leaves at seven time-points in a day to determine differentially expressed genes (DEGs). The biological processes and pathways with significant enrichment of DEGs were obtained. The DEGs in the QTL intervals were analyzed, and four flowering time-related candidate genes were found. These results lay a foundation for the genetic regulation of rapeseed flowering time and create a rapeseed gene expression library for seven time-points in a day.
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Affiliation(s)
- Jurong Song
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Bao Li
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Yanke Cui
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Chenjian Zhuo
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Yuanguo Gu
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
- Correspondence:
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20
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Jung H, Lee A, Jo SH, Park HJ, Jung WY, Kim HS, Lee HJ, Jeong SG, Kim YS, Cho HS. Nitrogen Signaling Genes and SOC1 Determine the Flowering Time in a Reciprocal Negative Feedback Loop in Chinese Cabbage ( Brassica rapa L.) Based on CRISPR/Cas9-Mediated Mutagenesis of Multiple BrSOC1 Homologs. Int J Mol Sci 2021; 22:ijms22094631. [PMID: 33924895 PMCID: PMC8124421 DOI: 10.3390/ijms22094631] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 11/29/2022] Open
Abstract
Precise flowering timing is critical for the plant life cycle. Here, we examined the molecular mechanisms and regulatory network associated with flowering in Chinese cabbage (Brassica rapa L.) by comparative transcriptome profiling of two Chinese cabbage inbred lines, “4004” (early bolting) and “50” (late bolting). RNA-Seq and quantitative reverse transcription PCR (qPCR) analyses showed that two positive nitric oxide (NO) signaling regulator genes, nitrite reductase (BrNIR) and nitrate reductase (BrNIA), were up-regulated in line “50” with or without vernalization. In agreement with the transcription analysis, the shoots in line “50” had substantially higher nitrogen levels than those in “4004”. Upon vernalization, the flowering repressor gene Circadian 1 (BrCIR1) was significantly up-regulated in line “50”, whereas the flowering enhancer genes named SUPPRESSOR OF OVEREXPRESSION OF CONSTANCE 1 homologs (BrSOC1s) were substantially up-regulated in line “4004”. CRISPR/Cas9-mediated mutagenesis in Chinese cabbage demonstrated that the BrSOC1-1/1-2/1-3 genes were involved in late flowering, and their expression was mutually exclusive with that of the nitrogen signaling genes. Thus, we identified two flowering mechanisms in Chinese cabbage: a reciprocal negative feedback loop between nitrogen signaling genes (BrNIA1 and BrNIR1) and BrSOC1s to control flowering time and positive feedback control of the expression of BrSOC1s.
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Affiliation(s)
- Haemyeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Seung Hee Jo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Hyun Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
| | - Won Yong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
- Department of Functional Genomics, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Seon-Geum Jeong
- Department of Biotechnology, NongWoo Bio, Anseong 17558, Korea;
| | - Youn-Sung Kim
- Department of Biotechnology, NongWoo Bio, Anseong 17558, Korea;
- Correspondence: (Y.-S.K.); (H.S.C.); Tel.: +82-31-652-5526 (Y.-S.K.); +82-42-860-4469 (H.S.C.)
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, Korea
- Correspondence: (Y.-S.K.); (H.S.C.); Tel.: +82-31-652-5526 (Y.-S.K.); +82-42-860-4469 (H.S.C.)
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21
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Wang L, Wang R, Lei W, Wu J, Li C, Shi H, Meng L, Yuan F, Zhou Q, Cui C. Transcriptome analysis reveals gene responses to herbicide, tribenuron methyl, in Brassica napus L. during seed germination. BMC Genomics 2021; 22:299. [PMID: 33892633 PMCID: PMC8067372 DOI: 10.1186/s12864-021-07614-1] [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: 11/20/2020] [Accepted: 04/14/2021] [Indexed: 11/25/2022] Open
Abstract
Background Tribenuron methyl (TBM) is an herbicide that inhibits sulfonylurea acetolactate synthase (ALS) and is one of the most widely used broad-leaved herbicides for crop production. However, soil residues or drifting of the herbicide spray might affect the germination and growth of rapeseed, Brassica napus, so it is imperative to understand the response mechanism of rape to TBM during germination. The aim of this study was to use transcriptome analysis to reveal the gene responses in herbicide-tolerant rapeseed to TBM stress during seed germination. Results 2414, 2286, and 1068 differentially expressed genes (DEGs) were identified in TBM-treated resistant vs sensitive lines, treated vs. control sensitive lines, treated vs. control resistant lines, respectively. GO analysis showed that most DEGs were annotated to the oxidation-reduction pathways and catalytic activity. KEGG enrichment was mainly involved in plant-pathogen interactions, α-linolenic acid metabolism, glucosinolate biosynthesis, and phenylpropanoid biosynthesis. Based on GO and KEGG enrichment, a total of 137 target genes were identified, including genes involved in biotransferase activity, response to antioxidant stress and lipid metabolism. Biotransferase genes, CYP450, ABC and GST, detoxify herbicide molecules through physical or biochemical processes. Antioxidant genes, RBOH, WRKY, CDPK, MAPK, CAT, and POD regulate plant tolerance by transmitting ROS signals and triggering antioxidant enzyme expression. Lipid-related genes and hormone-related genes were also found, such as LOX3, ADH1, JAZ6, BIN2 and ERF, and they also played an important role in herbicide resistance. Conclusions This study provides insights for selecting TBM-tolerant rapeseed germplasm and exploring the molecular mechanism of TBM tolerance during germination. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07614-1.
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Affiliation(s)
- Liuyan Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Ruili Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Wei Lei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Jiayi Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Chenyang Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Hongsong Shi
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Lijiao Meng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Fang Yuan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Qingyuan Zhou
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
| | - Cui Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
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Cheng S, Chen P, Su Z, Ma L, Hao P, Zhang J, Ma Q, Liu G, Liu J, Wang H, Wei H, Yu S. High-resolution temporal dynamic transcriptome landscape reveals a GhCAL-mediated flowering regulatory pathway in cotton (Gossypium hirsutum L.). PLANT BIOTECHNOLOGY JOURNAL 2021; 19:153-166. [PMID: 32654381 PMCID: PMC7769237 DOI: 10.1111/pbi.13449] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/24/2020] [Accepted: 05/19/2020] [Indexed: 05/04/2023]
Abstract
The transition from vegetative to reproductive growth is very important for early maturity in cotton. However, the genetic control of this highly dynamic and complex developmental process remains unclear. A high-resolution tissue- and stage-specific transcriptome profile was generated from six developmental stages using 72 samples of two early-maturing and two late-maturing cotton varieties. The results of histological analysis of paraffin sections showed that flower bud differentiation occurred at the third true leaf stage (3TLS) in early-maturing varieties, but at the fifth true leaf stage (5TLS) in late-maturing varieties. Using pairwise comparison and weighted gene co-expression network analysis, 5312 differentially expressed genes were obtained, which were divided into 10 gene co-expression modules. In the MElightcyan module, 46 candidate genes regulating cotton flower bud differentiation were identified and expressed at the flower bud differentiation stage. A novel key regulatory gene related to flower bud differentiation, GhCAL, was identified in the MElightcyan module. Anti-GhCAL transgenic cotton plants exhibited late flower bud differentiation and flowering time. GhCAL formed heterodimers with GhAP1-A04/GhAGL6-D09 and regulated the expression of GhAP1-A04 and GhAGL6-D09. GhAP1-A04- and GhAGL6-D09-silenced plants also showed significant late flowering. Finally, we propose a new flowering regulatory pathway mediated by GhCAL. This study elucidated the molecular mechanism of cotton flowering regulation and provides good genetic resources for cotton early-maturing breeding.
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Affiliation(s)
- Shuaishuai Cheng
- College of AgronomyNorthwest A&F UniversityYanglingChina
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Pengyun Chen
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Zhengzheng Su
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Liang Ma
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Pengbo Hao
- College of AgronomyNorthwest A&F UniversityYanglingChina
| | - Jingjing Zhang
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Qiang Ma
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Guoyuan Liu
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Ji Liu
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Hantao Wang
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Hengling Wei
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Shuxun Yu
- College of AgronomyNorthwest A&F UniversityYanglingChina
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
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Laoué J, Depardieu C, Gérardi S, Lamothe M, Bomal C, Azaiez A, Gros-Louis MC, Laroche J, Boyle B, Hammerbacher A, Isabel N, Bousquet J. Combining QTL Mapping and Transcriptomics to Decipher the Genetic Architecture of Phenolic Compounds Metabolism in the Conifer White Spruce. FRONTIERS IN PLANT SCIENCE 2021; 12:675108. [PMID: 34079574 PMCID: PMC8166253 DOI: 10.3389/fpls.2021.675108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/08/2021] [Indexed: 05/05/2023]
Abstract
Conifer forests worldwide are becoming increasingly vulnerable to the effects of climate change. Although the production of phenolic compounds (PCs) has been shown to be modulated by biotic and abiotic stresses, the genetic basis underlying the variation in their constitutive production level remains poorly documented in conifers. We used QTL mapping and RNA-Seq to explore the complex polygenic network underlying the constitutive production of PCs in a white spruce (Picea glauca) full-sib family for 2 years. QTL detection was performed for nine PCs and differentially expressed genes (DEGs) were identified between individuals with high and low PC contents for five PCs exhibiting stable QTLs across time. A total of 17 QTLs were detected for eight metabolites, including one major QTL explaining up to 91.3% of the neolignan-2 variance. The RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid biosynthesis, several key transcription factors, and a subset of 137 genes showing opposite expression patterns in individuals with high levels of the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs co-localized with QTLs. Our findings represent a significant step toward resolving the genomic architecture of PC production in spruce and facilitate the functional characterization of genes and transcriptional networks responsible for differences in constitutive production of PCs in conifers.
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Affiliation(s)
- Justine Laoué
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- *Correspondence: Justine Laoué
| | - Claire Depardieu
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Claude Bomal
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Aïda Azaiez
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Marie-Claude Gros-Louis
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Jérôme Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Almuth Hammerbacher
- Department of Zoology, Entomology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Nathalie Isabel
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Jean Bousquet
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Scheben A, Severn-Ellis AA, Patel D, Pradhan A, Rae SJ, Batley J, Edwards D. Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus. BMC PLANT BIOLOGY 2020; 20:546. [PMID: 33287721 PMCID: PMC7720618 DOI: 10.1186/s12870-020-02756-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/25/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Brassica napus is an important oilseed crop cultivated worldwide. During domestication and breeding of B. napus, flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering in B. napus. An F2 mapping population was derived from a cross between an early-flowering spring type and a late-flowering winter type. RESULTS Flowering time in the mapping population differed by up to 25 days between individuals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ~ 12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3981.31 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trait locus (QTL) on chromosome C2 was detected, covering eight flowering time genes including FLC. CONCLUSIONS These findings demonstrate the effectiveness of the ddRAD approach to sample the B. napus genome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F2 populations. Quality filtering and genotype correction and imputation can substantially reduce these error rates and allow effective linkage mapping and QTL analysis.
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Affiliation(s)
- Armin Scheben
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Anita A Severn-Ellis
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Dhwani Patel
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Aneeta Pradhan
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Stephen J Rae
- BASF Agricultural Solutions Belgium NV, BASF Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052, Ghent, Belgium
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.
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Cao X, Wang Y, Shu D, Qu H, Luo C, Hu X. Food intake-related genes in chicken determined through combinatorial genome-wide association study and transcriptome analysis. Anim Genet 2020; 51:741-751. [PMID: 32720725 DOI: 10.1111/age.12980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2020] [Indexed: 11/30/2022]
Abstract
The chicken gizzard is the primary digestive and absorptive organ regulating food intake and metabolism. Body weight is a typical complex trait regulated by an interactive polygene network which is under the control of an interacting network of polygenes. To simplify these genotype-phenotype associations, the gizzard is a suitable target organ to preliminarily explore the mechanism underlying the regulation of chicken growth through controlled food intake. This study aimed to identify key food intake-related genes through combinatorial GWAS and transcriptome analysis. We performed GWAS of body weight in an F2 intercrossed population and transcriptional profiling analysis of gizzards from chickens with different body weight. We identified a major 10 Mb quantitative trait locus (QTL) on chromosome 1 and numerous minor QTL distributed among 24 chromosomes. Combining data regarding QTL and gizzard gene expression, two hub genes, MLNR and HTR2A, and a list of core genes with small effect were found to be associated with food intake. Furthermore, the neuroactive ligand-receptor interaction pathway was found to play a key role in regulating the appetite of chickens. The present results show the major-minor gene interactions in metabolic pathways and provide insights into the genetic architecture and gene regulation during food intake in chickens.
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Affiliation(s)
- Xuemin Cao
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuzhe Wang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.,College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dingming Shu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Hao Qu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Chenglong Luo
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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Identification of Candidate Genes Involved in Curd Riceyness in Cauliflower. Int J Mol Sci 2020; 21:ijms21061999. [PMID: 32183438 PMCID: PMC7139996 DOI: 10.3390/ijms21061999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 11/23/2022] Open
Abstract
“Riceyness” refers to the precocious development of flower bud initials over the curd surface of cauliflower, and it is regarded as undesirable for the market. The present study aimed to identify the candidate loci and genes responsible for the morphological difference in riceyness between a pair of cauliflower sister lines. Genetic analysis revealed that riceyness is controlled by a single dominant locus. An F2 population derived from the cross between these sister lines was used to construct “riceyness” and “non-riceyness” bulks, and then it was subjected to BSA-seq. On the basis of the results of Δ(SNP-index) analysis, a 4.0 Mb candidate region including 22 putative SNPs was mapped on chromosome C04. Combining the RNA-seq, gene function annotation, and target sequence analysis among two parents and other breeding lines, an orthologous gene of the Arabidopsis gene SOC1, Bo4g024850 was presumed as the candidate gene, and an upstream SNP likely resulted in riceyness phenotype via influencing the expression levels of Bo4g024850. These results are helpful to understand the genetic mechanism regulating riceyness, and to facilitate the molecular improvement on cauliflower curds.
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Mamnabi S, Nasrollahzadeh S, Ghassemi-Golezani K, Raei Y. Improving yield-related physiological characteristics of spring rapeseed by integrated fertilizer management under water deficit conditions. Saudi J Biol Sci 2020; 27:797-804. [PMID: 32127754 PMCID: PMC7042669 DOI: 10.1016/j.sjbs.2020.01.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/17/2019] [Accepted: 01/06/2020] [Indexed: 11/19/2022] Open
Abstract
Two separate field experiments were conducted in 2018 and 2019 as split-plot based on randomized complete block design with three replications to evaluate physiological responses of rapeseed to fertilization treatments (control, chemical fertilizer, inoculation of seeds with PGPR, vermicompost and combined fertilizers) under different irrigation levels (irrigation after 70,100, 130, and 160 mm evaporation). Water stress increased the activities of catalase, polyphenol oxidase, peroxidase and superoxide dismutase and the contents of proline, soluble sugars and malondialdehyde and also leaf temperature, but decreased membrane stability index, chlorophyll content, leaf water content, stomatal conductance and grain yield. Application of fertilizers particularly combined fertilizers decreased proline content and leaf temperature, but increased the antioxidant enzymes activities, soluble sugars, chlorophyll content, leaf water content, membrane stability index, and stomatal conductance under different irrigation intervals. These superiorities of fertilization treatments were led to considerable improvement in grain yield. The results revealed that the combined fertilizer application improved most of the physiological parameters. It was deducted that the application of combined fertilizers reduced chemical fertilizer by about 67% and alleviated the deleterious effects of water limitation on field performance of rapeseed.
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Affiliation(s)
| | - Safar Nasrollahzadeh
- Department of Ecophysiology, Faculty of Agriculture, University of Tabriz, 5166614766 Tabriz, East Azarbayjan, Iran
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Schiessl S. Regulation and Subfunctionalization of Flowering Time Genes in the Allotetraploid Oil Crop Brassica napus. FRONTIERS IN PLANT SCIENCE 2020; 11:605155. [PMID: 33329678 PMCID: PMC7718018 DOI: 10.3389/fpls.2020.605155] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/29/2020] [Indexed: 05/03/2023]
Abstract
Flowering is a vulnerable, but crucial phase in building crop yield. Proper timing of this period is therefore decisive in obtaining optimal yields. However, genetic regulation of flowering integrates many different environmental signals and is therefore extremely complex. This complexity increases in polyploid crops which carry two or more chromosome sets, like wheat, potato or rapeseed. Here, I summarize the current state of knowledge about flowering time gene copies in rapeseed (Brassica napus), an important oil crop with a complex polyploid history and a close relationship to Arabidopsis thaliana. The current data show a high demand for more targeted studies on flowering time genes in crops rather than in models, allowing better breeding designs and a deeper understanding of evolutionary principles. Over evolutionary time, some copies of rapeseed flowering time genes changed or lost their original role, resulting in subfunctionalization of the respective homologs. For useful applications in breeding, such patterns of subfunctionalization need to be identified and better understood.
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Affiliation(s)
- Sarah Schiessl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
- *Correspondence: Sarah Schiessl,
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Xu Y, Zhang B, Ma N, Liu X, Qin M, Zhang Y, Wang K, Guo N, Zuo K, Liu X, Zhang M, Huang Z, Xu A. Quantitative Trait Locus Mapping and Identification of Candidate Genes Controlling Flowering Time in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2020; 11:626205. [PMID: 33613591 PMCID: PMC7886670 DOI: 10.3389/fpls.2020.626205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/30/2020] [Indexed: 05/02/2023]
Abstract
Flowering time plays a vital role in determining the life-cycle period, yield, and seed quality of rapeseed (Brassica napus L.) in certain environments. Quantitative trait locus (QTL) mapping to identify the genetic architecture of genes controlling flowering time helps accelerate the early maturity breeding process. In this study, simple sequence repeats (SSR) and specific-locus amplified fragment sequencing (SLAF-seq) technologies were adopted to map the QTLs for flowering time in four environments. As a result, three target intervals, FTA09, FTA10, and FTC05 were identified. Among this, FTA09 was considered as a novel interval, FTA10 and FTC05 as stable regions. Based on the parental re-sequencing data, 7,022 single nucleotide polymorphisms (SNPs) and 2,195 insertion-deletions (InDels) between the two parents were identified in these three target regions. A total of 186 genes possessed genetic variations in these intervals, 14 of which were related to flowering time involved in photoperiod, circadian clock, vernalization, and gibberellin pathways. Six InDel markers linked to flowering time were developed in the three target intervals, indicating that the results were credible in this study. These results laid a good foundation for further genetic studies on flowering-time regulation in B. napus L.
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Affiliation(s)
- Yu Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Bingbing Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Ning Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Xia Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
- Market Supervision Administration, Yanchi, China
| | - Mengfan Qin
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Yan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Kai Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Na Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Kaifeng Zuo
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Xiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Miao Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Zhen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
- Zhen Huang,
| | - Aixia Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
- *Correspondence: Aixia Xu,
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Sudan J, Singh R, Sharma S, Salgotra RK, Sharma V, Singh G, Sharma I, Sharma S, Gupta SK, Zargar SM. ddRAD sequencing-based identification of inter-genepool SNPs and association analysis in Brassica juncea. BMC PLANT BIOLOGY 2019; 19:594. [PMID: 31888485 PMCID: PMC6937933 DOI: 10.1186/s12870-019-2188-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/05/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Narrow genetic base, complex allo-tetraploid genome and presence of repetitive elements have led the discovery of single nucleotide polymorphisms (SNPs) in Brassica juncea (AABB; 2n = 4x = 36) at a slower pace. Double digest RAD (ddRAD) - a genome complexity reduction technique followed by NGS was used to generate a total of 23 million paired-end reads from three genotypes each of Indian (Pusa Tarak, RSPR-01 and Urvashi) and Exotic (Donskaja IV, Zem 1 and EC287711) genepools. RESULTS Sequence data analysis led to the identification of 10,399 SNPs in six genotypes at a read depth of 10x coverage among the genotypes of two genepools. A total of 44 hyper-variable regions (nucleotide variation hotspots) were also found in the genome, of which 93% were found to be a part of coding genes/regions. The functionality of the identified SNPs was estimated by genotyping a subset of SNPs on MassARRAY® platform among a diverse set of B. juncea genotypes. SNP genotyping-based genetic diversity and population studies placed the genotypes into two distinct clusters based mostly on the place of origin. The genotypes were also characterized for six morphological traits, analysis of which revealed a significant difference in the mean values between Indian and Exotic genepools for six traits. The association analysis for six traits identified a total of 45 significant marker-trait associations on 11 chromosomes of A- and B- group of progenitor genomes. CONCLUSIONS Despite narrow diversity, the ddRAD sequencing was able to identify large number of nucleotide polymorphisms between the two genepools. Association analysis led to the identification of common SNPs/genomic regions associated between flowering and maturity traits, thereby underscoring the possible role of common chromosomal regions-harboring genes controlling flowering and maturity in Brassica juncea.
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Affiliation(s)
- Jebi Sudan
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, J&K, India
- JECRC University- Jaipur, Jaipur, Rajasthan, India
| | - Ravinder Singh
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, J&K, India.
| | - Susheel Sharma
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, J&K, India
| | - Romesh K Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, J&K, India
| | - Varun Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K, India
| | - Gurvinder Singh
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K, India
| | - Indu Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K, India
| | - Swarkar Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K, India
| | - Surinder K Gupta
- Division of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jaipur, J&K, India
| | - Sajad Majeed Zargar
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu, J&K, India
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31
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Buchberger E, Reis M, Lu TH, Posnien N. Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies. Genes (Basel) 2019; 10:E492. [PMID: 31261769 PMCID: PMC6678813 DOI: 10.3390/genes10070492] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Accepted: 06/26/2019] [Indexed: 12/20/2022] Open
Abstract
Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic evolution. An exceptional contribution of cis-regulatory divergence has been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and stage-specific expression. We argue that the regulatory context must be considered in comparative expression studies.
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Affiliation(s)
- Elisa Buchberger
- University Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Dpt. of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
| | - Micael Reis
- University Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Dpt. of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
| | - Ting-Hsuan Lu
- University Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Dpt. of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
- International Max Planck Research School for Genome Science, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Nico Posnien
- University Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Dpt. of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
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Kim J, Manivannan A, Kim DS, Lee ES, Lee HE. Transcriptome sequencing assisted discovery and computational analysis of novel SNPs associated with flowering in Raphanus sativus in-bred lines for marker-assisted backcross breeding. HORTICULTURE RESEARCH 2019; 6:120. [PMID: 31700647 PMCID: PMC6823433 DOI: 10.1038/s41438-019-0200-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 05/08/2023]
Abstract
The sequencing of radish genome aids in the better understanding and tailoring of traits associated with economic importance. In order to accelerate the genomics assisted breeding and genetic selection, transcriptomes of 33 radish inbred lines with diverse traits were sequenced for the development of single nucleotide polymorphic (SNP) markers. The sequence reads ranged from 2,560,543,741 bp to 20,039,688,139 bp with the GC (%) of 47.80-49.34 and phred quality score (Q30) of 96.47-97.54%. A total of 4951 polymorphic SNPs were identified among the accessions after stringent filtering and 298 SNPs with efficient marker assisted backcross breeding (MAB) markers were generated from the polymorphic SNPs. Further, functional annotations of SNPs revealed the effects and importance of the SNPs identified in the flowering process. The SNPs were predominantly associated with the four major flowering related transcription factors such as MYB, MADS box (AG), AP2/EREB, and bHLH. In addition, SNPs in the vital flowering integrator gene (FT) and floral repressors (EMBRYONIC FLOWER 1, 2, and FRIGIDA) were identified among the radish inbred lines. Further, 50 SNPs were randomly selected from 298 SNPs and validated using Kompetitive Allele Specific PCR genotyping system (KASP) in 102 radish inbred lines. The homozygosity of the inbred lines varied from 56 to 96% and the phylogenetic analysis resulted in the clustering of inbred lines into three subgroups. Taken together, the SNP markers identified in the present study can be utilized for the discrimination, seed purity test, and adjusting parental combinations for breeding in radish.
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Affiliation(s)
- Jinhee Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Abinaya Manivannan
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Eun-Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
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