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Zhang L, Yang B, Li X, Chen S, Zhang C, Xiang S, Sun T, Yang Z, Kong X, Qu C, Lu K, Li J. Integrating GWAS, RNA-Seq and functional analysis revealed that BnaA02.SE mediates silique elongation by affecting cell proliferation and expansion in Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38899717 DOI: 10.1111/pbi.14413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/08/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024]
Abstract
Rapeseed (Brassica napus) silique is the major carbohydrate source for seed development, and the final silique length has attracted great attention from breeders. However, no studies had focused on the dynamic character of silique elongation length (SEL). Here, the dynamic SEL investigation in a natural population including 588 lines over two years indicate that dynamic SEL during 0-20 days after flowering was the most essential stage associated with seed number per silique (SPS) and thousand seed weight (TSW). Then, nine loci were identified to be associated with SEL based on GWAS analysis, among which five SNPs (over 50%) distributed on the A02 chromosome within 6.08 to 6.48 Mb. Subsequently, we screened 5078 differentially expressed genes between two extreme materials. An unknown protein, BnaA02.SE, was identified combining with GWAS and RNA-Seq analysis. Subcellular localization and expression profiles analysis demonstrated that BnaA02.SE is a chloroplast- and nucleus-localized protein mainly expressed in pericarps and leaves. Furthermore, transgenic verification and dynamic cytological observation reveal that overexpressed BnaA02.SE can promote silique elongation by regulating JA and IAA contents, affecting cell proliferation and expansion, respectively, and finally enhance seed yield by influencing SPS and TSW. Haplotype analysis reveal that the homologs of BnaA02.SE may also be involved in silique elongation regulation. Our findings provided comprehensive insights into a newly SEL trait, and cloned the first gene (BnaA02.SE) controlling silique elongation in B. napus. The identified BnaA02.SE and its homologs can offer a valuable target for improving B. napus yield.
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Affiliation(s)
- Liyuan Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Bo Yang
- Industrial Crops Research Institute, Yunnan Acedemy of Agricultural Sciences, Kunming, China
| | - Xiaodong Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Si Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Chao Zhang
- Oil Research Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Sirou Xiang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Tingting Sun
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Ziyan Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Xizeng Kong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Kun Lu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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Chen L, He W, Yu Y, Wang Y, Zhai X, Ling X, Lu P, Cheng X, Lei W, Fan Z. Molecular mapping and candidate gene identification of two major quantitative trait loci associated with silique length in oilseed rape ( Brassica napus L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:26. [PMID: 38516204 PMCID: PMC10951173 DOI: 10.1007/s11032-024-01464-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/12/2024] [Indexed: 03/23/2024]
Abstract
Rapeseed is a significant global source of plant oil. Silique size, particularly silique length (SL), impacts rapeseed yield. SL is a typical quantitative trait controlled by multiple genes. In our previous study, we constructed a DH population of 178 families known as the 158A-SGDH population. In this study, through SL QTL mapping, we identified twenty-six QTL for SL across five replicates in two environments. A QTL meta-analysis revealed eight consensus QTL, including two major QTL: cqSL.A02-1 (11.32-16.44% of PVE for SL), and cqSL.C06-1 (10.90-11.95% of PVE for SL). Based on biparental resequencing data and microcollinearity analysis of target regions in Brassica napus and Arabidopsis, we identified 11 candidate genes at cqSL.A02-1 and 6 candidate genes at cqSL.C06-1, which are potentially associated with silique development. Furthermore, transcriptome analysis of silique valves from both parents on the 14th, 21st, and 28th days after pollination (DAP) combined with gene function annotation revealed three significantly differentially expressed genes at cqSL.A02-1, BnaA02G0058500ZS, BnaA02G0060100ZS, and BnaA02G0060900ZS. Only the gene BnaC06G0283800ZS showed significant differences in parental transcription at cqSL.C06-1. Two tightly linked insertion-deletion markers for the cqSL.A02-1 and cqSL.C06-1 loci were developed. Using these two QTL, we generated four combinations: A02SGDH284C06158A, A02SGDH284C06SGDH284, A02158AC06158A, and A02158AC06SGDH284. Subsequent analysis identified an ideal QTL combination, A02158AC06SGDH284, which exhibited the longest SL of this type, reaching 6.06 ± 0.10 cm, significantly surpassing the other three combinations. The results will provide the basis for the cloning of SL-related genes of rapeseed, along with the development of functional markers of target genes and the breeding of rapeseed varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01464-x.
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Affiliation(s)
- Lei Chen
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Wangfei He
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Yulin Yu
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Yifan Wang
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Xueyang Zhai
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Xinxiang Ling
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Pan Lu
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Xinxin Cheng
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Weixia Lei
- Crop Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Zhixiong Fan
- Crop Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
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Susmitha P, Kumar P, Yadav P, Sahoo S, Kaur G, Pandey MK, Singh V, Tseng TM, Gangurde SS. Genome-wide association study as a powerful tool for dissecting competitive traits in legumes. FRONTIERS IN PLANT SCIENCE 2023; 14:1123631. [PMID: 37645459 PMCID: PMC10461012 DOI: 10.3389/fpls.2023.1123631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/08/2023] [Indexed: 08/31/2023]
Abstract
Legumes are extremely valuable because of their high protein content and several other nutritional components. The major challenge lies in maintaining the quantity and quality of protein and other nutritional compounds in view of climate change conditions. The global need for plant-based proteins has increased the demand for seeds with a high protein content that includes essential amino acids. Genome-wide association studies (GWAS) have evolved as a standard approach in agricultural genetics for examining such intricate characters. Recent development in machine learning methods shows promising applications for dimensionality reduction, which is a major challenge in GWAS. With the advancement in biotechnology, sequencing, and bioinformatics tools, estimation of linkage disequilibrium (LD) based associations between a genome-wide collection of single-nucleotide polymorphisms (SNPs) and desired phenotypic traits has become accessible. The markers from GWAS could be utilized for genomic selection (GS) to predict superior lines by calculating genomic estimated breeding values (GEBVs). For prediction accuracy, an assortment of statistical models could be utilized, such as ridge regression best linear unbiased prediction (rrBLUP), genomic best linear unbiased predictor (gBLUP), Bayesian, and random forest (RF). Both naturally diverse germplasm panels and family-based breeding populations can be used for association mapping based on the nature of the breeding system (inbred or outbred) in the plant species. MAGIC, MCILs, RIAILs, NAM, and ROAM are being used for association mapping in several crops. Several modifications of NAM, such as doubled haploid NAM (DH-NAM), backcross NAM (BC-NAM), and advanced backcross NAM (AB-NAM), have also been used in crops like rice, wheat, maize, barley mustard, etc. for reliable marker-trait associations (MTAs), phenotyping accuracy is equally important as genotyping. Highthroughput genotyping, phenomics, and computational techniques have advanced during the past few years, making it possible to explore such enormous datasets. Each population has unique virtues and flaws at the genomics and phenomics levels, which will be covered in more detail in this review study. The current investigation includes utilizing elite breeding lines as association mapping population, optimizing the choice of GWAS selection, population size, and hurdles in phenotyping, and statistical methods which will analyze competitive traits in legume breeding.
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Affiliation(s)
- Pusarla Susmitha
- Regional Agricultural Research Station, Acharya N.G. Ranga Agricultural University, Andhra Pradesh, India
| | - Pawan Kumar
- Department of Genetics and Plant Breeding, College of Agriculture, Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Pankaj Yadav
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Rajasthan, India
| | - Smrutishree Sahoo
- Department of Genetics and Plant Breeding, School of Agriculture, Gandhi Institute of Engineering and Technology (GIET) University, Odisha, India
| | - Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Manish K. Pandey
- Department of Genomics, Prebreeding and Bioinformatics, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Varsha Singh
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS, United States
| | - Te Ming Tseng
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS, United States
| | - Sunil S. Gangurde
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
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Bilgrami S, Darzi Ramandi H, Farokhzadeh S, Rousseau-Gueutin M, Sobhani Najafabadi A, Ghaderian M, Huang P, Liu L. Meta-analysis of seed weight QTLome using a consensus and highly dense genetic map in Brassica napus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:161. [PMID: 37354229 DOI: 10.1007/s00122-023-04401-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/02/2023] [Indexed: 06/26/2023]
Abstract
KEY MESSAGE We report here the discovery of high-confidence MQTL regions and of putative candidate genes associated with seed weight in B. napus using a highly dense consensus genetic map and by comparing various large-scale multiomics datasets. Seed weight (SW) is a direct determinant of seed yield in Brassica napus and is controlled by many loci. To unravel the main genomic regions associated with this complex trait, we used 13 available genetic maps to construct a consensus and highly dense map, comprising 40,401 polymorphic markers and 9191 genetic bins, harboring a cumulative length of 3047.8 cM. Then, we performed a meta-analysis using 639 projected SW quantitative trait loci (QTLs) obtained from studies conducted since 1999, enabling the identification of 57 meta-QTLS (MQTLs). The confidence intervals of our MQTLs were 9.8 and 4.3 times lower than the average CIs of the original QTLs for the A and C subgenomes, respectively, resulting in the detection of some key genes and several putative novel candidate genes associated with SW. By comparing the genes identified in MQTL intervals with multiomics datasets and coexpression analyses of common genes, we defined a more reliable and shorter list of putative candidate genes potentially involved in the regulation of seed maturation and SW. As an example, we provide a list of promising genes with high expression levels in seeds and embryos (e.g., BnaA03g04230D, BnaC03g08840D, BnaA10g29580D and BnaA03g27410D) that can be more finely studied through functional genetics experiments or that may be useful for MQTL-assisted breeding for SW. The high-density genetic consensus map and the single nucleotide polymorphism (SNP) physical map generated from the latest B. napus cv. Darmor-bzh v10 assembly will be a valuable resource for further mapping and map-based cloning of other important traits.
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Affiliation(s)
- Sayedehsaba Bilgrami
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Hadi Darzi Ramandi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Sara Farokhzadeh
- Department of Plant Production, College of Agriculture and Natural Resources of Darab, Shiraz University, Darab, Iran
| | | | - Ahmad Sobhani Najafabadi
- Department of Biotechnology, Agricultural Biotechnology Research Institute of Iran - Isfahan Branch, Agricultural Research, Education and Extension Organization (AREEO), Isfahan, Iran
| | - Mostafa Ghaderian
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
| | - Pu Huang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China.
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Ma Z, Du R, Xie J, Sun D, Fang H, Jiang L, Cen H. Phenotyping of Silique Morphology in Oilseed Rape Using Skeletonization with Hierarchical Segmentation. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0027. [PMID: 36939450 PMCID: PMC10017417 DOI: 10.34133/plantphenomics.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Silique morphology is an important trait that determines the yield output of oilseed rape (Brassica napus L.). Segmenting siliques and quantifying traits are challenging because of the complicated structure of an oilseed rape plant at the reproductive stage. This study aims to develop an accurate method in which a skeletonization algorithm was combined with the hierarchical segmentation (SHS) algorithm to separate siliques from the whole plant using 3-dimensional (3D) point clouds. We combined the L1-median skeleton with the random sample consensus for iteratively extracting skeleton points and optimized the skeleton based on information such as distance, angle, and direction from neighborhood points. Density-based spatial clustering of applications with noise and weighted unidirectional graph were used to achieve hierarchical segmentation of siliques. Using the SHS, we quantified the silique number (SN), silique length (SL), and silique volume (SV) automatically based on the geometric rules. The proposed method was tested with the oilseed rape plants at the mature stage grown in a greenhouse and field. We found that our method showed good performance in silique segmentation and phenotypic extraction with R 2 values of 0.922 and 0.934 for SN and total SL, respectively. Additionally, SN, total SL, and total SV had the statistical significance of correlations with the yield of a plant, with R values of 0.935, 0.916, and 0.897, respectively. Overall, the SHS algorithm is accurate, efficient, and robust for the segmentation of siliques and extraction of silique morphological parameters, which is promising for high-throughput silique phenotyping in oilseed rape breeding.
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Affiliation(s)
- Zhihong Ma
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| | - Ruiming Du
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| | - Jiayang Xie
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| | - Dawei Sun
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| | - Hui Fang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| | - Lixi Jiang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, P.R. China
| | - Haiyan Cen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
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Yang M, Chen J, Chang Y, Wan S, Zhao Z, Ni F, Guan R. Fine Mapping of a Pleiotropic Locus ( BnUD1) Responsible for the Up-Curling Leaves and Downward-Pointing Siliques in Brassica napus. Int J Mol Sci 2023; 24:ijms24043069. [PMID: 36834480 PMCID: PMC9965582 DOI: 10.3390/ijms24043069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 02/08/2023] Open
Abstract
Leaves and siliques are important organs associated with dry matter biosynthesis and vegetable oil accumulation in plants. We identified and characterized a novel locus controlling leaf and silique development using the Brassica napus mutant Bnud1, which has downward-pointing siliques and up-curling leaves. The inheritance analysis showed that the up-curling leaf and downward-pointing silique traits are controlled by one dominant locus (BnUD1) in populations derived from NJAU5773 and Zhongshuang 11. The BnUD1 locus was initially mapped to a 3.99 Mb interval on the A05 chromosome with a BC6F2 population by a bulked segregant analysis-sequencing approach. To more precisely map BnUD1, 103 InDel primer pairs uniformly covering the mapping interval and the BC5F3 and BC6F2 populations consisting of 1042 individuals were used to narrow the mapping interval to a 54.84 kb region. The mapping interval included 11 annotated genes. The bioinformatic analysis and gene sequencing data suggested that BnaA05G0157900ZS and BnaA05G0158100ZS may be responsible for the mutant traits. Protein sequence analyses showed that the mutations in the candidate gene BnaA05G0157900ZS altered the encoded PME in the trans-membrane region (G45A), the PMEI domain (G122S), and the pectinesterase domain (G394D). In addition, a 573 bp insertion was detected in the pectinesterase domain of the BnaA05G0157900ZS gene in the Bnud1 mutant. Other primary experiments indicated that the locus responsible for the downward-pointing siliques and up-curling leaves negatively affected the plant height and 1000-seed weight, but it significantly increased the seeds per silique and positively affected photosynthetic efficiency to some extent. Furthermore, plants carrying the BnUD1 locus were compact, implying they may be useful for increasing B. napus planting density. The findings of this study provide an important foundation for future research on the genetic mechanism regulating the dicotyledonous plant growth status, and the Bnud1 plants can be used directly in breeding.
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Mutari B, Sibiya J, Shayanowako A, Chidzanga C, Matova PM, Gasura E. Genome-wide association mapping for component traits of drought tolerance in dry beans (Phaseolus vulgaris L.). PLoS One 2023; 18:e0278500. [PMID: 37200295 DOI: 10.1371/journal.pone.0278500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/30/2023] [Indexed: 05/20/2023] Open
Abstract
Understanding the genetic basis of traits of economic importance under drought stressed and well-watered conditions is important in enhancing genetic gains in dry beans (Phaseolus vulgaris L.). This research aims to: (i) identify markers associated with agronomic and physiological traits for drought tolerance and (ii) identify drought-related putative candidate genes within the mapped genomic regions. An andean and middle-american diversity panel (AMDP) comprising of 185 genotypes was screened in the field under drought stressed and well-watered conditions for two successive seasons. Agronomic and physiological traits, viz., days to 50% flowering (DFW), plant height (PH), days to physiological maturity (DPM), grain yield (GYD), 100-seed weight (SW), leaf temperature (LT), leaf chlorophyll content (LCC) and stomatal conductance (SC) were phenotyped. Principal component and association analysis were conducted using the filtered 9370 Diversity Arrays Technology sequencing (DArTseq) markers. The mean PH, GYD, SW, DPM, LCC and SC of the panel was reduced by 12.1, 29.6, 10.3, 12.6, 28.5 and 62.0%, respectively under drought stressed conditions. Population structure analysis revealed two sub-populations, which corresponded to the andean and middle-american gene pools. Markers explained 0.08-0.10, 0.22-0.23, 0.29-0.32, 0.43-0.44, 0.65-0.66 and 0.69-0.70 of the total phenotypic variability (R2) for SC, LT, PH, GYD, SW and DFW, respectively under drought stressed conditions. For well-watered conditions, R2 varied from 0.08 (LT) to 0.70 (DPM). Overall, 68 significant (p < 10-03) marker-trait associations (MTAs) and 22 putative candidate genes were identified across drought stressed and well-watered conditions. Most of the identified genes had known biological functions related to regulating the response to drought stress. The findings provide new insights into the genetic architecture of drought stress tolerance in common bean. The findings also provide potential candidate SNPs and putative genes that can be utilized in gene discovery and marker-assisted breeding for drought tolerance after validation.
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Affiliation(s)
- Bruce Mutari
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
- Department of Research and Specialist Services, Crop Breeding Institute, Harare, Zimbabwe
| | - Julia Sibiya
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Admire Shayanowako
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Charity Chidzanga
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, Australia
| | | | - Edmore Gasura
- University of Zimbabwe, Mt Pleasant, Harare, Zimbabwe
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Systematic trait dissection in oilseed rape provides a comprehensive view, further insight, and exact roadmap for yield determination. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:38. [PMID: 35440054 PMCID: PMC9019968 DOI: 10.1186/s13068-022-02134-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/03/2022] [Indexed: 11/10/2022]
Abstract
Background Yield is the most important and complex trait that is influenced by numerous relevant traits with very complicated interrelations. While there are a large number of studies on the phenotypic relationship and genetic basis of yield traits, systematic studies with further dissection focusing on yield are limited. Therefore, there is still lack of a comprehensive and in-depth understanding of the determination of yield. Results In this study, yield was systematically dissected at the phenotypic, genetic to molecular levels in oilseed rape (Brassica napus L.). The analysis of correlation, network, and principal component for 21 traits in BnaZN-RIL population showed that yield was determined by a complex trait network with key contributors. The analysis of the constructed high-density single nucleotide polymorphism (SNP) linkage map revealed the concentrated distribution of distorted and heterozygous markers, likely due to selection on genes controlling the growth period and yield heterosis. A total of 134 consensus quantitative trait loci (QTL) were identified for 21 traits, of which all were incorporated into an interconnecting QTL network with dozens of hub-QTL. Four representative hub-QTL were further dissected to the target or candidate genes that governed the causal relationships between the relevant traits. Conclusions The highly consistent results at the phenotypic, genetic, and molecular dissecting demonstrated that yield was determined by a multilayer composite network that involved numerous traits and genes showing complex up/down-stream and positive/negative regulation. This provides a systematic view, further insight, and exact roadmap for yield determination, which represents a significant advance toward the understanding and dissection of complex traits. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02134-w.
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Xiong H, Wang R, Jia X, Sun H, Duan R. Transcriptomic analysis of rapeseed ( Brassica napus. L.) seed development in Xiangride, Qinghai Plateau, reveals how its special eco-environment results in high yield in high-altitude areas. FRONTIERS IN PLANT SCIENCE 2022; 13:927418. [PMID: 35982704 PMCID: PMC9379305 DOI: 10.3389/fpls.2022.927418] [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: 04/24/2022] [Accepted: 07/01/2022] [Indexed: 06/12/2023]
Abstract
As one of the most important oil crops, rapeseed (Brassica napus) is cultivated worldwide to produce vegetable oil, animal feed, and biodiesel. As the population grows and the need for renewable energy increases, the breeding and cultivation of high-yield rapeseed varieties have become top priorities. The formation of a high rapeseed yield is so complex because it is influenced not only by genetic mechanisms but also by many environmental conditions, such as climatic conditions and different farming practices. Interestingly, many high-yield areas are located in special eco-environments, for example, in the high-altitude Xiangride area of the Qinghai Plateau. However, the molecular mechanisms underlying the formation of high yields in such a special eco-environment area remain largely unknown. Here, we conducted field yield analysis and transcriptome analysis in the Xiangride area. Compared with the yield and environmental factors in the Xinning area (a low-yielding area), we found that the relatively longer daylight length is the key to high rapeseed yield in the Xiangride area, which leads up to a 52.1% increase in rapeseed yield, especially the increase in thousand seed weight and silique number (SN). Combined with transcriptome H-cluster analysis and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses, we can assume that the grain development of rapeseed in the Xiangride area is ahead of schedule and lasts for a long time, leading to the high-yield results in the Xiangride area, confirmed by the expression analysis by quantitative real-time polymerase chain reaction (qRT-PCR) of yield-related genes. Our results provide valuable information for further exploring the molecular mechanism underlying high yield in special ecological environments and provide a helpful reference for studying seed development characteristics in special-producing regions for Brassica napus.
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Affiliation(s)
- Huiyan Xiong
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Ruisheng Wang
- Academy of Agricultural and Forestry Sciences of Qinghai University, Key Laboratory of Spring Rape Genetic Improvement of Qinghai Province, Rapeseed Research and Development Center of Qinghai Province, Xining, China
| | - Xianqing Jia
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Hezhe Sun
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Ruijun Duan
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
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A Preliminary Study for Identifying Quantitative Trait Loci Associated with Seed Production in Radish Using Genotyping-by-Sequencing. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8030268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
The high yield of seeds can reduce the cost of seed production for parental lines, as well as F1 cultivars in radish. The number of seeds per silique and silique length are two important traits among traits determining seed yield, but no study has been conducted on their quantitative trait loci (QTLs) in radish. A high-density linkage map was constructed, based on genotyping-by-sequencing (GBS) of the F2 population, derived from two parental lines, significantly differed by the two traits, which were grown in a controlled environment to minimize the environmental effects. Using the map with 848 SNPs, three significant QTLs were identified, two and one of which were associated with the number of seeds per silique and silique length, respectively. Ortholog analysis was conducted with Arabidopsis thaliana genes, related to the number of seeds per silique, and revealed five radish putative candidate genes. These putative candidate genes appear to be related to ovule, embryo sac, embryo, pollen and seed development, as well as a double fertilization process. The method to pollinate the F2 population, as well as preliminary QTLs and SNPs therein, can be helpful for future QTL studies to improve seed production in radish breeding programs.
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11
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Sun T, Zhang Y. MAP kinase cascades in plant development and immune signaling. EMBO Rep 2022; 23:e53817. [PMID: 35041234 PMCID: PMC8811656 DOI: 10.15252/embr.202153817] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/26/2021] [Accepted: 01/01/2022] [Indexed: 02/05/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) cascades are important signaling modules regulating diverse biological processes. During the past 20 years, much progress has been made on the functions of MAPK cascades in plants. This review summarizes the roles of MAPKs, known MAPK substrates, and our current understanding of MAPK cascades in plant development and innate immunity. In addition, recent findings on the molecular links connecting surface receptors to MAPK cascades and the mechanisms underlying MAPK signaling specificity are also discussed.
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Affiliation(s)
- Tongjun Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Yuelin Zhang
- Department of BotanyUniversity of British ColumbiaVancouverBCCanada
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12
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Zhou X, Zhang H, Wang P, Liu Y, Zhang X, Song Y, Wang Z, Ali A, Wan L, Yang G, Hong D. BnaC7.ROT3, the causal gene of cqSL-C7, mediates silique length by affecting cell elongation in Brassica napus. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:154-167. [PMID: 34486674 DOI: 10.1093/jxb/erab407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 09/05/2021] [Indexed: 06/13/2023]
Abstract
Siliques are a major carbohydrate source of energy for later seed development in rapeseed (Brassica napus). Thus, silique length has received great attention from breeders. We previously detected a novel quantitative trait locus cqSL-C7 that controls silique length in B. napus. Here, we further validated the cqSL-C7 locus and isolated its causal gene (BnaC7.ROT3) by map-based cloning. In 'Zhongshuang11' (parent line with long siliques), BnaC7.ROT3 encodes the potential cytochrome P450 monooxygenase CYP90C1, whereas in 'G120' (parent line with short siliques), a single nucleotide deletion in the fifth exon of BnaC7.ROT3 results in a loss-of-function truncated protein. Sub-cellular localization and expression pattern analysis revealed that BnaC7.ROT3 is a membrane-localized protein mainly expressed in leaves, flowers and siliques. Cytological observations showed that the cells in silique walls of BnaC7.ROT3-transformed positive plants were longer than those of transgene-negative plants in the background of 'G120', suggesting that BnaC7.ROT3 affects cell elongation. Haplotype analysis demonstrated that most alleles of BnaC7.ROT3 are favorable in B. napus germplasms, and its homologs may also be involved in silique length regulation. Our findings provide novel insights into the regulatory mechanisms of natural silique length variations and valuable genetic resources for the improvement of silique length in rapeseed.
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Affiliation(s)
- Xianming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Haiyan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ying Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaohui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yixian Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhaoyang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ahmad Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lili Wan
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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13
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Wang J, Fan Y, Mao L, Qu C, Lu K, Li J, Liu L. Genome-wide association study and transcriptome analysis dissect the genetic control of silique length in Brassica napus L. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:214. [PMID: 34743746 PMCID: PMC8573943 DOI: 10.1186/s13068-021-02064-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/25/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Rapeseed is the third-largest oilseed crop after soybeans and palm that produces vegetable oil for human consumption and biofuel for industrial production. Silique length (SL) is an important trait that is strongly related to seed yield in rapeseed. Although many studies related to SL have been reported in rapeseed, only a few candidate genes have been found and cloned, and the genetic mechanisms regulating SL in rapeseed remain unclear. Here, we dissected the genetic basis of SL by genome-wide association studies (GWAS) combined with transcriptome analysis. RESULTS We identified quantitative trait locus (QTL) for SL using a recombinant inbred line (RIL) population and two independent GWAS populations. Major QTLs on chromosomes A07, A09, and C08 were stably detected in all environments from all populations. Several candidate genes related to starch and sucrose metabolism, plant hormone signal transmission and phenylpropanoid biosynthesis were detected in the main QTL intervals, such as BnaA9.CP12-2, BnaA9.NST2, BnaA7.MYB63, and BnaA7.ARF17. In addition, the results of RNA-seq and weighted gene co-expression network analysis (WGCNA) showed that starch and sucrose metabolism, photosynthesis, and secondary cell wall biosynthesis play an important role in the development of siliques. CONCLUSIONS We propose that photosynthesis, sucrose and starch metabolism, plant hormones, and lignin content play important roles in the development of rapeseed siliques.
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Affiliation(s)
- Jia Wang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, China
| | - Yueling Fan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, China
| | - Lin Mao
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, China.
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14
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Khan SU, Saeed S, Khan MHU, Fan C, Ahmar S, Arriagada O, Shahzad R, Branca F, Mora-Poblete F. Advances and Challenges for QTL Analysis and GWAS in the Plant-Breeding of High-Yielding: A Focus on Rapeseed. Biomolecules 2021; 11:1516. [PMID: 34680149 PMCID: PMC8533950 DOI: 10.3390/biom11101516] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Yield is one of the most important agronomic traits for the breeding of rapeseed (Brassica napus L), but its genetic dissection for the formation of high yield remains enigmatic, given the rapid population growth. In the present review, we review the discovery of major loci underlying important agronomic traits and the recent advancement in the selection of complex traits. Further, we discuss the benchmark summary of high-throughput techniques for the high-resolution genetic breeding of rapeseed. Biparental linkage analysis and association mapping have become powerful strategies to comprehend the genetic architecture of complex agronomic traits in crops. The generation of improved crop varieties, especially rapeseed, is greatly urged to enhance yield productivity. In this sense, the whole-genome sequencing of rapeseed has become achievable to clone and identify quantitative trait loci (QTLs). Moreover, the generation of high-throughput sequencing and genotyping techniques has significantly enhanced the precision of QTL mapping and genome-wide association study (GWAS) methodologies. Furthermore, this study demonstrates the first attempt to identify novel QTLs of yield-related traits, specifically focusing on ovule number per pod (ON). We also highlight the recent breakthrough concerning single-locus-GWAS (SL-GWAS) and multi-locus GWAS (ML-GWAS), which aim to enhance the potential and robust control of GWAS for improved complex traits.
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Affiliation(s)
- Shahid Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Sumbul Saeed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Muhammad Hafeez Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3465548, Chile;
| | - Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile;
| | - Raheel Shahzad
- Department of Biotechnology, Faculty of Science & Technology, Universitas Muhammadiyah Bandung, Bandung 40614, Indonesia;
| | - Ferdinando Branca
- Department of Agriculture, Food and Environment (Di3A), University of Catania, 95123 Catania, Italy;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3465548, Chile;
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15
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Xin S, Dong H, Yang L, Huang D, Zheng F, Cui Y, Wu S, Liao J, He Y, Wan H, Liu Z, Li X, Qian W. Both overlapping and independent loci underlie seed number per pod and seed weight in Brassica napus by comparative quantitative trait loci analysis. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:41. [PMID: 37309442 PMCID: PMC10236046 DOI: 10.1007/s11032-021-01232-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/10/2021] [Indexed: 06/14/2023]
Abstract
Seed number per pod (SNPP) and seed weight (SW) are two components of seed yield in rapeseed (Brassica napus). Here, a natural population of rapeseed was employed for genome-wide association analysis for SNPP and SW across multi-years. A total of 101 and 77 SNPs significantly associated with SNPP and SW with the phenotypic variances (R2) ranging from 1.35 to 29.47% and from 0.78 to 34.58%, respectively. And 43 and 33 homologs of known genes from model plants were located in the 65 and 49 haplotype blocks (HBs) for SNPP and SW, respectively. Notably, we found 5 overlapping loci and 3 sets of loci with collinearity for both SNPP and SW, of which 4 overlapping loci harbored the haplotypes with the same direction of genetic effects on SNPP and SW, indicating high possibility to simultaneously improve SNPP and SW in rapeseed. Our findings revealed both overlapping and independent loci controlling seed number per pod and seed weight in rapeseed. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01232-1.
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Affiliation(s)
- Shuangshuang Xin
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Hongli Dong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Lei Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Dengwen Huang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Fajing Zheng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Shuang Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Jinghang Liao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Huafang Wan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Zhi Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Xiaorong Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715 China
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16
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Chen X, Tong C, Zhang X, Song A, Hu M, Dong W, Chen F, Wang Y, Tu J, Liu S, Tang H, Zhang L. A high-quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:615-630. [PMID: 33073445 PMCID: PMC7955885 DOI: 10.1111/pbi.13493] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 09/21/2020] [Accepted: 10/13/2020] [Indexed: 05/03/2023]
Abstract
Rapeseed (Brassica napus L.) is a recent allotetraploid crop, which is well known for its high oil production. Here, we report a high-quality genome assembly of a typical semi-winter rapeseed cultivar, 'Zhongshuang11' (hereafter 'ZS11'), using a combination of single-molecule sequencing and chromosome conformation capture (Hi-C) techniques. Most of the high-confidence sequences (93.1%) were anchored to the individual chromosomes with a total of 19 centromeres identified, matching the exact chromosome count of B. napus. The repeat sequences in the A and C subgenomes in B. napus expanded significantly from 500 000 years ago, especially over the last 100 000 years. These young and recently amplified LTR-RTs showed dispersed chromosomal distribution but significantly preferentially clustered into centromeric regions. We exhaustively annotated the nucleotide-binding leucine-rich repeat (NLR) gene repertoire, yielding a total of 597 NLR genes in B. napus genome and 17.4% of which are paired (head-to-head arrangement). Based on the resequencing data of 991 B. napus accessions, we have identified 18 759 245 single nucleotide polymorphisms (SNPs) and detected a large number of genomic regions under selective sweep among the three major ecotype groups (winter, semi-winter and spring) in B. napus. We found 49 NLR genes and five NLR gene pairs colocated in selective sweep regions with different ecotypes, suggesting a rapid diversification of NLR genes during the domestication of B. napus. The high quality of our B. napus 'ZS11' genome assembly could serve as an important resource for the study of rapeseed genomics and reveal the genetic variations associated with important agronomic traits.
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Affiliation(s)
- Xuequn Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural Affairs of PRCOil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanChina
| | - Xingtan Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Aixia Song
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Ming Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural Affairs of PRCOil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanChina
| | - Wei Dong
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Fei Chen
- College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhouChina
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic ImprovementNational Center of Rapeseed ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural Affairs of PRCOil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanChina
| | - Haibao Tang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Liangsheng Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
- Genomics and Genetic Engineering Laboratory of Ornamental PlantsCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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17
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Wang H, Yan M, Xiong M, Wang P, Liu Y, Xin Q, Wan L, Yang G, Hong D. Genetic dissection of thousand-seed weight and fine mapping of cqSW.A03-2 via linkage and association analysis in rapeseed (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1321-1335. [PMID: 32002584 DOI: 10.1007/s00122-020-03553-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE: cqSW.A03-2, one of the six identified quantitative trait loci associated with thousand-seed weight in rapeseed, is mapped to a 61.6-kb region on chromosome A03 and corresponds to the candidate gene BnaA03G37960D. Seed weight is an important factor that determines the seed yield of oilseed rape (Brassica napus L.). To elucidate the genetic mechanism of thousand-seed weight (TSW), quantitative trait locus (QTL) mapping was conducted using a double haploid population derived from the cross between an elite line ZY50 and a pol cytoplasmic male sterility restorer line 7-5. The genetic basis of TSW was dissected into six major QTLs. One major QTL denoted as cqSW.A03-2, which explained 8.46-13.70% of the phenotypic variation, was detected across multiple environments. To uncover the genetic basis of cqSW.A03-2, a set of near-isogenic lines were developed. Based on the test of self-pollinated progenies, cqSW.A03-2 was identified as a single Mendelian factor and the ZY50 allele at cqSW.A03-2 showed a positive effect on TSW. Fine mapping delimited the cqSW.A03-2 locus into a 61.6-kb region, and 18 genes within this region were predicted. Candidate gene association analysis and expression analysis indicated that a histidine kinase gene (BnaA03G37960D) is likely to be the candidate gene for the cqSW.A03-2 locus. Our results may contribute to a better understanding of the molecular mechanism of seed weight regulation and promote the breeding program for yield improvement in rapeseed.
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Affiliation(s)
- Hao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Min Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mei Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ying Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, China
| | - Qiang Xin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lili Wan
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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18
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Shen W, Qin P, Yan M, Li B, Wu Z, Wen J, Yi B, Ma C, Shen J, Fu T, Tu J. Fine mapping of a silique length- and seed weight-related gene in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2985-2996. [PMID: 31321475 DOI: 10.1007/s00122-019-03400-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
Using microarray analysis combined with map-based cloning, a major locus positively regulating SL and SW was mapped to a 98.47 kb interval on A09 in rapeseed. In rapeseed, seed yield is closely associated with silique-related traits such as silique length (SL) and seed weight (SW). Previously identified quantitative trait loci (QTLs) revealed that SL and SW are complex traits and many QTLs overlap. However, the genetic characterization of the association between SL and SW is poorly understood. In the present study, a BC3F3 near isogenic line developed from a short silique plant and the long silique cultivar 'ZS11' was analyzed to identify the locus related to SL. Map-based cloning indicated that a major locus acting as a single Mendelian factor was mapped to a 98.47 kb region on chromosome A09. BLAST analysis and DNA sequencing showed SNP variations and a fragment replacement in the upstream region of the candidate gene BnaA09g55530D may alter gene expression and influence SL. The results showed that this SL locus may also positively affect SW as well as in the 186 rapeseed accessions identified by the associated markers. Therefore, selecting plants with appropriate SL and developing functional markers for the associated gene could play important roles in the molecular breeding of high-yield rapeseed varieties.
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Affiliation(s)
- Wenhao Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pei Qin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengjiao Yan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bao Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zengxiang Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China.
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19
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Shi L, Song J, Guo C, Wang B, Guan Z, Yang P, Chen X, Zhang Q, King GJ, Wang J, Liu K. A CACTA-like transposable element in the upstream region of BnaA9.CYP78A9 acts as an enhancer to increase silique length and seed weight in rapeseed. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:524-539. [PMID: 30664290 DOI: 10.1111/tpj.14236] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/13/2019] [Accepted: 01/18/2019] [Indexed: 05/26/2023]
Abstract
Rapeseed (Brassica napus L.) is a model plant for polyploid crop research and the second-leading source of vegetable oil worldwide. Silique length (SL) and seed weight are two important yield-influencing traits in rapeseed. Using map-based cloning, we isolated qSLWA9, which encodes a P450 monooxygenase (BnaA9.CYP78A9) and functions as a positive regulator of SL. The expression level of BnaA9.CYP78A9 in silique valves of the long-silique variety is much higher than that in the regular-silique variety, which results in elongated cells and a prolonged phase of silique elongation. Plants of the long-silique variety and transgenic plants with high expression of BnaA9.CYP78A9 had a higher concentration of auxin in the developing silique; this induced a number of auxin-related genes but no genes in well-known auxin biosynthesis pathways, suggesting that BnaA9.CYP78A9 may influence auxin concentration by affecting auxin metabolism or an unknown auxin biosynthesis pathway. A 3.7-kb CACTA-like transposable element (TE) inserted in the 3.9-kb upstream regulatory sequence of BnaA9.CYP78A9 elevates the expression level, suggesting that the CACTA-like TE acts as an enhancer to stimulate high gene expression and silique elongation. Marker and sequence analysis revealed that the TE in B. napus had recently been introgressed from Brassica rapa by interspecific hybridization. The insertion of the TE is consistently associated with long siliques and large seeds in both B. napus and B. rapa collections. However, the frequency of the CACTA-like TE in rapeseed varieties is still very low, suggesting that this allele has not been widely used in rapeseed breeding programs and would be invaluable for yield improvement in rapeseed breeding.
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Affiliation(s)
- Liuliu Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jurong Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chaocheng Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhilin Guan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Pu Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xun Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Li N, Song D, Peng W, Zhan J, Shi J, Wang X, Liu G, Wang H. Maternal control of seed weight in rapeseed (Brassica napus L.): the causal link between the size of pod (mother, source) and seed (offspring, sink). PLANT BIOTECHNOLOGY JOURNAL 2019; 17:736-749. [PMID: 30191657 PMCID: PMC6419582 DOI: 10.1111/pbi.13011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 08/26/2018] [Accepted: 09/04/2018] [Indexed: 05/16/2023]
Abstract
Seed size/weight is one of the key traits related to plant domestication and crop improvement. In rapeseed (Brassica napus L.) germplasm, seed weight shows extensive variation, but its regulatory mechanism is poorly understood. To identify the key mechanism of seed weight regulation, a systematic comparative study was performed. Genetic, morphological and cytological evidence showed that seed weight was controlled by maternal genotype, through the regulation of seed size mainly via cell number. The physiological evidence indicated that differences in the pod length might result in differences in pod wall photosynthetic area, carbohydrates and the final seed weight. We also identified two pleiotropic major quantitative trait loci that acted indirectly on seed weight via their effects on pod length. RNA-seq results showed that genes related to pod development and hormones were significantly differentially expressed in the pod wall; genes related to development, cell division, nutrient reservoir and ribosomal proteins were all up-regulated in the seeds of the large-seed pool. Finally, we proposed a potential seed weight regulatory mechanism that is specific to rapeseed and novel in plants. The results demonstrate a causal link between the size of the pod (mother, source) and the seed (offspring, sink) in rapeseed, which provides novel insight into the maternal control of seed weight and will open a new research field in plants.
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Affiliation(s)
- Na Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
- Zhengzhou Fruit Research Institute of the Chinese Academy of Agricultural SciencesThe Laboratory of Melon CropsZhengzhouHenan ProvinceChina
| | - Dongji Song
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Wei Peng
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Jiepeng Zhan
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Jiaqin Shi
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Guihua Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
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21
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Mapping loci controlling fatty acid profiles, oil and protein content by genome-wide association study in Brassica napus. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2018.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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22
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Wang H, Zaman QU, Huang W, Mei D, Liu J, Wang W, Ding B, Hao M, Fu L, Cheng H, Hu Q. QTL and Candidate Gene Identification for Silique Length Based on High-Dense Genetic Map in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2019; 10:1579. [PMID: 31850044 PMCID: PMC6895753 DOI: 10.3389/fpls.2019.01579] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/12/2019] [Indexed: 05/13/2023]
Abstract
Silique length (SL) is an important yield trait and positively correlates with seeds per silique and seed weight. In the present study, two double haploid (DH) populations, established from crosses Zhongshuang11 × R11 (ZR) and R1 × R2 (RR), containing 280 and 95 DH lines, respectively, were used to map quantitative trait loci (QTL) for SL. A high-dense genetic map from ZR population was constructed comprising 14,658 bins on 19 linkage groups, with map length of 2,198.85 cM and an average marker distance of 0.15 cM. Genetic linkage map from RR population was constructed by using 2,046 mapped markers anchored to 19 chromosomes with 2,217-cM map length and an average marker distance of 1.08 cM. Major QTL qSL_ZR_A09 and qSL_RR_A09b on A09 were identified from ZR and RR populations, respectively. Both QTL could be stably detected in four environments. QTL qSL_RR_A09b and qSL_ZR_A09 were located on 68.5-70.8 cM and 91.33-91.94 cM interval with R2 values of 14.99-39.07% and 15.00-20.36% in RR and ZR populations, respectively. Based on the physical positions of single nucleotide polymorphism (SNP) markers flanking qSL_ZR_A09 and gene annotation in Arabidopsis, 26 genes were identified with SNP/Indel variation between parents and two genes (BnaA09g41180D and BnaA09g41380D) were selected as the candidate genes. Expression analysis further revealed BnaA09g41180D, encoding homologs of Arabidopsis fasciclin-like arabinogalactan proteins (FLA3), as the most promising candidate gene for qSL_ZR_A09. The QTL identification and candidate gene analysis will provide new insight into the genomic regions controlling SL in Brassica napus as well as candidate genes underlying the QTL.
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Affiliation(s)
- Hui Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qamar U. Zaman
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
- Graduate School of the Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenhui Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Desheng Mei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jia Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Wenxiang Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Bingli Ding
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Mengyu Hao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Li Fu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Hongtao Cheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
- *Correspondence: Hongtao Cheng ; Qiong Hu
| | - Qiong Hu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
- *Correspondence: Hongtao Cheng ; Qiong Hu
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Yang S, Zhang B, Liu G, Hong B, Xu J, Chen X, Wang B, Wu Z, Hou F, Yue X, Wang J, Zhang Q, King GJ, Liu K. A comprehensive and precise set of intervarietal substitution lines to identify candidate genes and quantitative trait loci in oilseed rape (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2117-2129. [PMID: 29998372 DOI: 10.1007/s00122-018-3140-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/01/2018] [Indexed: 06/08/2023]
Abstract
A set of intervarietal substitution lines were developed in rapeseed by recurrent backcrossing and marker-assisted selection and employed for mapping both qualitative and quantitative traits. Intervarietal substitution lines (ISLs) may be assembled into advanced secondary mapping populations that have remarkable potential for resolving trait loci and mapping candidate genes. To facilitate the identification of important genes in oilseed rape (canola, Brassica napus), we developed 89 ISLs using an elite cultivar 'Zhongyou 821' (ZY821) as the recipient and a re-synthesized line 'No.2127' as the donor. In the whole process of ISLs development, the target chromosome segments were selected based on the genotypes of 300 microsatellite markers evenly distributed across the genome. Eighty-nine ISLs fixed at BC5F4 were genotyped by sequencing using double digestion to survey the lengths of target substitution segments from the donor parent and the background segments from the recurrent parent. The total length of the substituted chromosome segments was 3030.27 Mb, representing 3.56 × of the Darmor-bzh reference genome sequence (version 4.1). Gene mapping was conducted for two qualitative traits, flower colour and seed-coat colour, and nine quantitative traits including yield- and quality-related traits, with 19 QTLs identified for the latter. Overlapping substitution segments were identified for flower colour and seed-coat colour loci, as well as for QTLs consistently detected in 2 or 3 years. These results demonstrate the value of these ISLs for locus resolution and subsequent cloning, targeted mutation or editing of genes controlling important traits in oilseed rape.
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Affiliation(s)
- Shanjing Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bao Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gang Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Baohua Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinsong Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xun Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhikun Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fan Hou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaopeng Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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25
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Rahaman M, Mamidi S, Rahman M. Genome-wide association study of heat stress-tolerance traits in spring-type Brassica napus L. under controlled conditions. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.cj.2017.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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26
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Yu M, Liu Z, Jiang S, Xu N, Chen Q, Qi Z, Lv W. QTL mapping and candidate gene mining for soybean seed weight per plant. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1438851] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Meng Yu
- College of Agriculture Department, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Zhangxiong Liu
- Institute of Crop Sciences Department, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Shanshan Jiang
- College of Agriculture Department, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Ning Xu
- Heilongjiang Academy of Land Reclamation Sciences, Harbin, Heilongjiang, PR China
| | - Qingshan Chen
- College of Agriculture Department, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Zhaoming Qi
- College of Agriculture Department, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Wenhe Lv
- College of Agriculture Department, Northeast Agricultural University, Harbin, Heilongjiang, PR China
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27
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Kulwal PL. Trait Mapping Approaches Through Linkage Mapping in Plants. PLANT GENETICS AND MOLECULAR BIOLOGY 2018; 164:53-82. [DOI: 10.1007/10_2017_49] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Dong H, Tan C, Li Y, He Y, Wei S, Cui Y, Chen Y, Wei D, Fu Y, He Y, Wan H, Liu Z, Xiong Q, Lu K, Li J, Qian W. Genome-Wide Association Study Reveals Both Overlapping and Independent Genetic Loci to Control Seed Weight and Silique Length in Brassica napus. FRONTIERS IN PLANT SCIENCE 2018; 9:921. [PMID: 30073005 PMCID: PMC6058094 DOI: 10.3389/fpls.2018.00921] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/11/2018] [Indexed: 05/13/2023]
Abstract
Seed weight (SW) is one of three determinants of seed yield, which positively correlates with silique length (SL) in Brassica napus (rapeseed). However, the genetic mechanism underlying the relationship between seed weight (SW) and silique length (SL) is largely unknown at present. A natural population comprising 157 inbred lines in rapeseed was genotyped by whole-genome re-sequencing and investigated for SW and SL over four years. The genome-wide association study identified 20 SNPs in significant association with SW on A01, A04, A09, C02, and C06 chromosomes and the phenotypic variation explained by a single locus ranged from 11.85% to 34.58% with an average of 25.43%. Meanwhile, 742 SNPs significantly associated with SL on A02, A03, A04, A07, A08, A09, C01, C03, C04, C06, C07, and C08 chromosomes were also detected and the phenotypic variation explained by a single locus ranged from 4.01 to 48.02% with an average of 33.33%, out of which, more than half of the loci had not been reported in the previous studies. There were 320 overlapping or linked SNPs for both SW and SL on A04, A09, and C06 chromosomes. It indicated that both overlapping and independent genetic loci controlled both SW and SL in B. napus. On the haplotype block on A09 chromosome, the allele variants of a known gene BnaA.ARF18.a controlling both SW and SL were identified in the natural population by developing derived cleaved amplified polymorphic sequence (dCAPS) markers. These findings are valuable for understanding the genetic mechanism of SW and SL and also for rapeseed molecular breeding programs.
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Affiliation(s)
- Hongli Dong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Chuandong Tan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yuzhen Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yan He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Shuai Wei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yangui Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Dayong Wei
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Ying Fu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Huafang Wan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Zhi Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Qing Xiong
- School of Computer and Information Science, Southwest University, Chongqing, China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- *Correspondence: Wei Qian
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Wang Z, Huai D, Zhang Z, Cheng K, Kang Y, Wan L, Yan L, Jiang H, Lei Y, Liao B. Development of a High-Density Genetic Map Based on Specific Length Amplified Fragment Sequencing and Its Application in Quantitative Trait Loci Analysis for Yield-Related Traits in Cultivated Peanut. FRONTIERS IN PLANT SCIENCE 2018; 9:827. [PMID: 29997635 PMCID: PMC6028809 DOI: 10.3389/fpls.2018.00827] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 05/28/2018] [Indexed: 05/20/2023]
Abstract
High-density genetic maps (HDGMs) are very useful for genomic studies and quantitative trait loci (QTL) mapping. However, the low frequency of DNA polymorphisms in peanut has limited the quantity of available markers and hindered the construction of a HDGM. This study generated a peanut genetic map with the highest number of high-quality SNPs based on specific locus amplified fragment sequencing (SLAF-seq) technology and a newly constructed RIL population ("ZH16" × "sd-H1"). The constructed HDGM included 3,630 SNP markers belonging to 2,636 bins on 20 linkage groups (LGs), and it covers 2,098.14 cM in length, with an average marker distance of 0.58 cM. This HDGM was applied for the following collinear comparison, scaffold anchoring and analysis of genomic characterization including recombination rates and segregation distortion in peanut. For QTL mapping of investigated 14 yield-related traits, a total of 62 QTLs were detected on 12 chromosomes across 3 environments, and the co-localization of QTLs was observed for these traits which were significantly correlated on phenotype. Two stable co-located QTLs for seed- and pod-related traits were significantly identified in the chromosomal end of B06 and B07, respectively. The construction of HDGM and QTL analysis for yield-related traits in this study provide useful information for fine mapping and functional analysis of genes as well as molecular marker-assisted breeding.
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Shen Y, Xiang Y, Xu E, Ge X, Li Z. Major Co-localized QTL for Plant Height, Branch Initiation Height, Stem Diameter, and Flowering Time in an Alien Introgression Derived Brassica napus DH Population. FRONTIERS IN PLANT SCIENCE 2018; 9:390. [PMID: 29643859 PMCID: PMC5883169 DOI: 10.3389/fpls.2018.00390] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/12/2018] [Indexed: 05/18/2023]
Abstract
Plant height (PH), branch initiation height (BIH), and stem diameter (SD) are three stem-related traits that play crucial roles in plant architecture and lodging resistance. Herein, we show one doubled haploid (DH) population obtained from a cross between Y689 (one Capsella bursa-pastoris derived Brassica napus intertribal introgression) and Westar (B. napus cultivar) that these traits were significantly positively correlated with one another and with flowering time (FT). Based on a high-density SNP map, a total of 102 additive quantitative trait loci (QTL) were identified across six environments. Seventy-two consensus QTL and 49 unique QTL were identified using a two-round strategy of QTL meta-analysis. Notably, a total of 19 major QTL, including 11 novel ones, were detected for these traits, which comprised two QTL clusters on chromosomes A02 and A07. Conditional QTL mapping was performed to preliminarily evaluate the genetic basis (pleiotropy or tight linkage) of the co-localized QTL. In addition, QTL by environment interactions (QEI) mapping was performed to verify the additive QTL and estimate the QEI effect. In the genomic regions of all major QTL, orthologs of the genes involved in phytohormone biosynthesis, phytohormone signaling, flower development, and cell differentiation in Arabidopsis were proposed as candidate genes. Of these, BnaA02g02560, an ortholog of Arabidopsis GASA4, was suggested as a candidate gene for PH, SD, and FT; and BnaA02g08490, an ortholog of Arabidopsis GNL, was associated with PH, BIH and FT. These results provide useful information for further genetic studies on stem-related traits and plant growth adaptation.
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Affiliation(s)
- Yusen Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Yusen Shen
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Ensheng Xu
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Zaiyun Li
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Sun F, Fan G, Hu Q, Zhou Y, Guan M, Tong C, Li J, Du D, Qi C, Jiang L, Liu W, Huang S, Chen W, Yu J, Mei D, Meng J, Zeng P, Shi J, Liu K, Wang X, Wang X, Long Y, Liang X, Hu Z, Huang G, Dong C, Zhang H, Li J, Zhang Y, Li L, Shi C, Wang J, Lee SMY, Guan C, Xu X, Liu S, Liu X, Chalhoub B, Hua W, Wang H. The high-quality genome of Brassica napus cultivar 'ZS11' reveals the introgression history in semi-winter morphotype. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:452-468. [PMID: 28849613 DOI: 10.1111/tpj.13669] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/05/2017] [Accepted: 08/11/2017] [Indexed: 05/04/2023]
Abstract
Allotetraploid oilseed rape (Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B. napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi-winter oilseed rape cultivar 'ZS11' and its comprehensive genomic comparison with the genomes of the winter-type cultivar 'Darmor-bzh' as well as two progenitors. The integrated BAC-to-BAC and whole-genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high-quality genome assembly of B. napus 'ZS11'. Within a short evolutionary period (~6700 years ago), semi-winter-type 'ZS11' and the winter-type 'Darmor-bzh' maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to 'Darmor-bzh', both two subgenomes of 'ZS11' are closely related to its progenitors, and the 'ZS11' genome harbored several specific segmental homoeologous exchanges (HEs). Furthermore, the semi-winter-type 'ZS11' underwent potential genomic introgressions with B. rapa (Ar ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.FLC3 regulating vernalization-responsive flowering time in 'ZS11' was first experienced HE, and then underwent genomic introgression event with Ar , which potentially has led to genetic differences in controlling vernalization in the semi-winter types. Our observations improved our understanding of the genetic diversity of different B. napus morphotypes and the cultivation history of semi-winter oilseed rape in Asia.
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Affiliation(s)
- Fengming Sun
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Guangyi Fan
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, Qingdao, 266555, China
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China
| | - Qiong Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mei Guan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, BeiBei District, Chongqing, 400715, China
| | - Dezhi Du
- Qinghai Academy of Agricultural and Forestry, National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, 810016, China
| | - Cunkou Qi
- Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Liangcai Jiang
- Shichun Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Weiqing Liu
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Shunmou Huang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Wenbin Chen
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Jingyin Yu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Desheng Mei
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Peng Zeng
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Jiaqin Shi
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xi Wang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Xinfa Wang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinming Liang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Zhiyong Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Guodong Huang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Caihua Dong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - He Zhang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Jun Li
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yaolei Zhang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Liangwei Li
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Chengcheng Shi
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Jiahao Wang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China
| | - Chunyun Guan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Xun Xu
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xin Liu
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, Qingdao, 266555, China
| | - Boulos Chalhoub
- Institut National de Recherche Agronomique (INRA), Unité de Recherche en Génomique Végétale (URGV), UMR1165, Organization and Evolution of Plant Genomes (OEPG), 2 rue Gaston Crémieux, 91057, Evry, France
| | - Wei Hua
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Hanzhong Wang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
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Luo Z, Wang M, Long Y, Huang Y, Shi L, Zhang C, Liu X, Fitt BDL, Xiang J, Mason AS, Snowdon RJ, Liu P, Meng J, Zou J. Incorporating pleiotropic quantitative trait loci in dissection of complex traits: seed yield in rapeseed as an example. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1569-1585. [PMID: 28455767 PMCID: PMC5719798 DOI: 10.1007/s00122-017-2911-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 04/19/2017] [Indexed: 05/10/2023]
Abstract
A comprehensive linkage atlas for seed yield in rapeseed. Most agronomic traits of interest for crop improvement (including seed yield) are highly complex quantitative traits controlled by numerous genetic loci, which brings challenges for comprehensively capturing associated markers/genes. We propose that multiple trait interactions underlie complex traits such as seed yield, and that considering these component traits and their interactions can dissect individual quantitative trait loci (QTL) effects more effectively and improve yield predictions. Using a segregating rapeseed (Brassica napus) population, we analyzed a large set of trait data generated in 19 independent experiments to investigate correlations between seed yield and other complex traits, and further identified QTL in this population with a SNP-based genetic bin map. A total of 1904 consensus QTL accounting for 22 traits, including 80 QTL directly affecting seed yield, were anchored to the B. napus reference sequence. Through trait association analysis and QTL meta-analysis, we identified a total of 525 indivisible QTL that either directly or indirectly contributed to seed yield, of which 295 QTL were detected across multiple environments. A majority (81.5%) of the 525 QTL were pleiotropic. By considering associations between traits, we identified 25 yield-related QTL previously ignored due to contrasting genetic effects, as well as 31 QTL with minor complementary effects. Implementation of the 525 QTL in genomic prediction models improved seed yield prediction accuracy. Dissecting the genetic and phenotypic interrelationships underlying complex quantitative traits using this method will provide valuable insights for genomics-based crop improvement.
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Affiliation(s)
- Ziliang Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Meng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yongju Huang
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB UK
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiang Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Bruce D. L. Fitt
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB UK
| | - Jinxia Xiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Annaliese S. Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Peifa Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
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Chen J, Wang B, Zhang Y, Yue X, Li Z, Liu K. High-density ddRAD linkage and yield-related QTL mapping delimits a chromosomal region responsible for oil content in rapeseed ( Brassica napus L.). BREEDING SCIENCE 2017; 67:296-306. [PMID: 28744183 PMCID: PMC5515304 DOI: 10.1270/jsbbs.16116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 04/06/2017] [Indexed: 05/04/2023]
Abstract
Rapeseed (Brassica napus L.) is one of the most important oil crops almost all over the world. Seed-related traits, including oil content (OC), silique length (SL), seeds per silique (SS), and seed weight (SW), are primary targets for oil yield improvement. To dissect the genetic basis of these traits, 192 recombinant inbred lines (RILs) were derived from two parents with distinct oil content and silique length. High-density linkage map with a total length of 1610.4 cM were constructed using 1,329 double-digestion restriction site associated DNA (ddRAD) markers, 107 insertion/deletions (INDELs), and 90 well-distributed simple sequence repeats (SSRs) markers. A total of 37 consensus quantitative trait loci (QTLs) were detected for the four traits, with individual QTL explained 3.1-12.8% of the phenotypic variations. Interestingly, one OC consensus QTL (cqOCA10b) on chromosome A10 was consistently detected in all three environments, and explained 9.8% to 12.8% of the OC variation. The locus was further delimited into an approximately 614 kb genomic region, in which the flanking markers could be further evaluated for marker-assisted selection in rapeseed OC improvement and the candidate genes targeted for map-based cloning and genetic manipulation.
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Ju M, Zhou Z, Mu C, Zhang X, Gao J, Liang Y, Chen J, Wu Y, Li X, Wang S, Wen J, Yang L, Wu J. Dissecting the genetic architecture of Fusarium verticillioides seed rot resistance in maize by combining QTL mapping and genome-wide association analysis. Sci Rep 2017; 7:46446. [PMID: 28422143 PMCID: PMC5396065 DOI: 10.1038/srep46446] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 03/17/2017] [Indexed: 01/22/2023] Open
Abstract
Fusarium verticillioides can be transmitted via seeds and cause systemic infection in maize (Zea mays L.); its mycotoxin has harmful effects on animal and human health. We combined QTL mapping in recombinant inbred line (RIL) populations with a genome-wide association study (GWAS) of 217 diverse maize lines using 224,152 single nucleotide polymorphisms (SNPs) under controlled conditions to determine the genetic architecture of F. verticillioides seed rot (FSR) resistance. Our study identified 8 quantitative trait loci (QTLs) and 43 genes associated with 57 SNPs that were correlated with FSR resistance through linkage mapping and GWAS, respectively. Among these, there were three candidate genes, namely GRMZM2G0081223, AC213654.3_FG004, and GRMZM2G099255, which were detected in both linkage mapping and GWAS. Furthermore, the near-isogenic lines (NILs) containing GRMZM2G0081223, which also had a susceptible parent background, were found to have a significantly improved level of resistance. In addition, the expression profile of the three candidate genes revealed that they all respond to the infection following inoculation with F. verticillioides. These genetic analyses indicate that FSR resistance is controlled by loci with minor effect, and the polymerization breeding of lines with beneficial alleles and candidate genes could improve FSR resistance in maize.
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Affiliation(s)
- Ming Ju
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zijian Zhou
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Cong Mu
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuecai Zhang
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jingyang Gao
- College of Life sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Yakun Liang
- College of Life sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiafa Chen
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yabin Wu
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaopeng Li
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Shiwei Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jingjing Wen
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Luming Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Jianyu Wu
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
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Dhaka N, Rout K, Yadava SK, Sodhi YS, Gupta V, Pental D, Pradhan AK. Genetic dissection of seed weight by QTL analysis and detection of allelic variation in Indian and east European gene pool lines of Brassica juncea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:293-307. [PMID: 27744489 DOI: 10.1007/s00122-016-2811-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/08/2016] [Indexed: 05/26/2023]
Abstract
Seed weight QTL identified in different populations were synthesized into consensus QTL which were shown to harbor candidate genes by in silico mapping. Allelic variation inferred would be useful in breeding B. juncea lines with high seed weight. Seed weight is an important yield influencing trait in oilseed Brassicas and is a multigenic trait. Among the oilseed Brassicas, Brassica juncea harbors the maximum phenotypic variation wherein thousand seed weight varies from around 2.0 g to more than 7.0 g. In this study, we have undertaken quantitative trait locus/quantitative trait loci (QTL) analysis of seed weight in B. juncea using four bi-parental doubled-haploid populations. These four populations were derived from six lines (three Indian and three east European lines) with parental phenotypic values for thousand seed weight ranging from 2.0 to 7.6 g in different environments. Multi-environment QTL analysis of the four populations identified a total of 65 QTL ranging from 10 to 25 in each population. Meta-analysis of these component QTL of the four populations identified six 'consensus' QTL (C-QTL) in A3, A7, A10 and B3 by merging 33 of the 65 component Tsw QTL from different bi-parental populations. Allelic diversity analysis of these six C-QTL showed that Indian lines, Pusajaikisan and Varuna, hold the most positive allele in all the six C-QTL. In silico mapping of candidate genes with the consensus QTL localized 11 genes known to influence seed weight in Arabidopsis thaliana and also showed conserved crucifer blocks harboring seed weight QTL between the A subgenomes of B. juncea and B. rapa. These findings pave the way for a better understanding of the genetics of seed weight in the oilseed crop B. juncea and reveal the scope available for improvement of seed weight through marker-assisted breeding.
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Affiliation(s)
- Namrata Dhaka
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Kadambini Rout
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Satish K Yadava
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Yaspal Singh Sodhi
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Vibha Gupta
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Akshay K Pradhan
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
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Ye J, Yang Y, Chen B, Shi J, Luo M, Zhan J, Wang X, Liu G, Wang H. An integrated analysis of QTL mapping and RNA sequencing provides further insights and promising candidates for pod number variation in rapeseed (Brassica napus L.). BMC Genomics 2017; 18:71. [PMID: 28077071 PMCID: PMC5225578 DOI: 10.1186/s12864-016-3402-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 12/09/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND As the most important yield component in rapeseed (Brassica napus L.), pod number is determined by a series of successive growth and development processes. Pod number shows extensive variation in rapeseed natural germplasm, which is valuable for genetic improvement. However, the genetic and especially the molecular mechanism for this kind of variation are poorly understood. In this study, we conducted QTL mapping and RNA sequencing, respectively, using the BnaZNRIL population and its two parental cultivars Zhongshuang11 and No.73290 which showed significant difference in pod number, primarily due to the difference in floral organ number. RESULT A total of eight QTLs for pod number were identified using BnaZNRIL population with a high-density SNP linkage map, each was distributed on seven linkage groups and explained 5.8-11.9% of phenotypic variance. Then, they were integrated with those previously detected in BnaZNF2 population (deriving from same parents) and resulted in 15 consensus-QTLs. Of which, seven QTLs were identical to other studies, whereas the other eight should be novel. RNA sequencing of the shoot apical meristem (SAM) at the formation stage of floral bud primordia identified 9135 genes that were differentially expressed between the two parents. Gene ontology (GO) analysis showed that the top two enriched groups were S-assimilation, providing an essential nutrient for the synthesis of diverse metabolites, and polyamine metabolism, serving as second messengers that play an essential role in flowering genes initiation. KEGG analysis showed that the top three overrepresented pathways were carbohydrate (707 genes), amino acid (390 genes) and lipid metabolisms (322 genes). In silico mapping showed that 647 DEGs were located within the confidence intervals of 15 consensus QTLs. Based on annotations of Arabidopsis homologs corresponding to DEGs, nine genes related to meristem growth and development were considered as promising candidates for six QTLs. CONCLUSION In this study, we discovered the first repeatable major QTL for pod number in rapeseed. In addition, RNA sequencing was performed for SAM in rapeseed, which provides new insights into the determination of floral organ number. Furthermore, the integration of DEGs and QTLs identified promising candidates for further gene cloning and mechanism study.
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Affiliation(s)
- Jiang Ye
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Yuhua Yang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Bo Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiaqin Shi
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China.
| | - Meizhong Luo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiepeng Zhan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Guihua Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China.
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Yang Y, Shen Y, Li S, Ge X, Li Z. High Density Linkage Map Construction and QTL Detection for Three Silique-Related Traits in Orychophragmus violaceus Derived Brassica napus Population. FRONTIERS IN PLANT SCIENCE 2017; 8:1512. [PMID: 28932230 PMCID: PMC5592274 DOI: 10.3389/fpls.2017.01512] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/16/2017] [Indexed: 05/08/2023]
Abstract
Seeds per silique (SS), seed weight (SW), and silique length (SL) are important determinant traits of seed yield potential in rapeseed (Brassica napus L.), and are controlled by naturally occurring quantitative trait loci (QTLs). Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. Orychophragmus violaceus is a crucifer with long siliques, many SS, and heavy seeds. A novel B. napus introgression line with many SS was previously selected from multiple crosses (B. rapa ssp. chinesis × O. violaceus) × B. napus. In present study, a doubled haploid (DH) population with 167 lines was established from a cross between the introgression line and a line with far fewer SS, in order to detect QTLs for silique-related traits. By screening with a Brassica 60K single nucleotide polymorphism (SNP) array, a high-density linkage map consisting of 1,153 bins and spanning a cumulative length of 2,209.1 cM was constructed, using 12,602 high-quality polymorphic SNPs in the DH population. The average recombination bin densities of the A and C subgenomes were 1.7 and 2.4 cM, respectively. 45 QTLs were identified for the three traits in all, which explained 4.0-34.4% of the total phenotypic variation; 20 of them were integrated into three unique QTLs by meta-analysis. These unique QTLs revealed a significant positive correlation between SS and SL and a significant negative correlation between SW and SS, and were mapped onto the linkage groups A05, C08, and C09. A trait-by-trait meta-analysis revealed eight, four, and seven consensus QTLs for SS, SW, and SL, respectively, and five major QTLs (cqSS.A09b, cqSS.C09, cqSW.A05, cqSW.C09, and cqSL.C09) were identified. Five, three, and four QTLs for SS, SW, and SL, respectively, might be novel QTLs because of the existence of alien genetic loci for these traits in the alien introgression. Thirty-eight candidate genes underlying nine QTLs for silique-related traits were identified.
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Chen Y, Ren X, Zheng Y, Zhou X, Huang L, Yan L, Jiao Y, Chen W, Huang S, Wan L, Lei Y, Liao B, Huai D, Wei W, Jiang H. Genetic mapping of yield traits using RIL population derived from Fuchuan Dahuasheng and ICG6375 of peanut ( Arachis hypogaea L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2017; 37:17. [PMID: 28216998 PMCID: PMC5285419 DOI: 10.1007/s11032-016-0587-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 11/01/2016] [Indexed: 05/04/2023]
Abstract
The genetic architecture determinants of yield traits in peanut (Arachis hypogaea L.) are poorly understood. In the present study, an effort was made to map quantitative trait loci (QTLs) for yield traits using recombinant inbred lines (RIL). A genetic linkage map was constructed containing 609 loci, covering a total of 1557.48 cM with an average distance of 2.56 cM between adjacent markers. The present map exhibited good collinearity with the physical map of diploid species of Arachis. Ninety-two repeatable QTLs were identified for 11 traits including height of main stem, total branching number, and nine pod- and seed-related traits. Of the 92 QTLs, 15 QTLs were expressed across three environments and 65 QTLs were newly identified. Twelve QTLs for the height of main stem and the pod- and seed-related traits explaining more than 10 % of phenotypic variation showed a great potential for marker-assisted selection in improving these traits. The trait-by-trait meta-analysis revealed 33 consensus QTLs. The consensus QTLs and other QTLs were further integrated into 29 pleiotropic unique QTLs with the confidence interval of 1.86 cM on average. The significant co-localization of QTLs was consistent with the significant phenotypic correlations among these traits. The complexity of the genetic architecture of yield traits was demonstrated. The present QTLs for pod- and seed-related traits could be the most fundamental genetic factors contributing to the yield traits in peanut. The results provide a good foundation for fine mapping, cloning and designing molecular breeding of favorable genes in peanut.
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Affiliation(s)
- Yuning Chen
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Xiaoping Ren
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Yanli Zheng
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Xiaojing Zhou
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Li Huang
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Liying Yan
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Yongqing Jiao
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Weigang Chen
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Shunmou Huang
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Liyun Wan
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Yong Lei
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Boshou Liao
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Dongxin Huai
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Wenhui Wei
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Huifang Jiang
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
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Chen L, An Y, Li YX, Li C, Shi Y, Song Y, Zhang D, Wang T, Li Y. Candidate Loci for Yield-Related Traits in Maize Revealed by a Combination of MetaQTL Analysis and Regional Association Mapping. FRONTIERS IN PLANT SCIENCE 2017; 8:2190. [PMID: 29312420 PMCID: PMC5744402 DOI: 10.3389/fpls.2017.02190] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/12/2017] [Indexed: 05/05/2023]
Abstract
Maize grain yield and related traits are complex and are controlled by a large number of genes of small effect or quantitative trait loci (QTL). Over the years, a large number of yield-related QTLs have been identified in maize and deposited in public databases. However, integrating and re-analyzing these data and mining candidate loci for yield-related traits has become a major issue in maize. In this study, we collected information on QTLs conferring maize yield-related traits from 33 published studies. Then, 999 of these QTLs were iteratively projected and subjected to meta-analysis to obtain metaQTLs (MQTLs). A total of 76 MQTLs were found across the maize genome. Based on a comparative genomics strategy, several maize orthologs of rice yield-related genes were identified in these MQTL regions. Furthermore, three potential candidate genes (Gene ID: GRMZM2G359974, GRMZM2G301884, and GRMZM2G083894) associated with kernel size and weight within three MQTL regions were identified using regional association mapping, based on the results of the meta-analysis. This strategy, combining MQTL analysis and regional association mapping, is helpful for functional marker development and rapid identification of candidate genes or loci.
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Raman H, Raman R, McVittie B, Orchard B, Qiu Y, Delourme R. A Major Locus for Manganese Tolerance Maps on Chromosome A09 in a Doubled Haploid Population of Brassica napus L. FRONTIERS IN PLANT SCIENCE 2017; 8:1952. [PMID: 29312361 PMCID: PMC5733045 DOI: 10.3389/fpls.2017.01952] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/30/2017] [Indexed: 05/09/2023]
Abstract
Soil acidity poses a major threat to productivity of several crops; mainly due to the prevalence of toxic levels of Al3+ and Mn2+. Crop productivity could be harnessed on acid soils via the development of plant varieties tolerant to phytotoxic levels of these cations. In this study, we investigated the extent of natural variation for Mn2+ tolerance among ten parental lines of the Australian and International canola mapping populations. Response to Mn2+ toxicity was measured on the bases of cotyledon chlorosis, shoot biomass, and leaf area in nutrient solution under control (9 μM of MnCl2⋅4H2O) and Mn treatment (125 μM of MnCl2⋅4H2O). Among parental lines, we selected Darmor-bzh and Yudal that showed significant and contrasting variation in Mn2+ tolerance to understand genetic control and identify the quantitative trait loci (QTL) underlying Mn2+ tolerance. We evaluated parental lines and their doubled haploid (DH) progenies (196 lines) derived from an F1 cross, Darmor-bzh/Yudal for Mn2+ tolerance. Mn2+-tolerant genotypes had significantly higher shoot biomass and leaf area compared to Mn2+-sensitive genotypes. A genetic linkage map based on 7,805 DArTseq markers corresponding to 2,094 unique loci was constructed and further utilized for QTL identification. A major locus, BnMn2+.A09 was further mapped with a SNP marker, Bn-A09-p29012402 (LOD score of 34.6) accounting for most of the variation in Mn2+ tolerance on chromosome A09. This is the first report on the genomic localization of a Mn2+ tolerance locus in B. napus. Additionally, an ortholog of A. thaliana encoding for cation efflux facilitator transporter was located within 3,991 bp from significant SNP marker associated with BnMn2+.A09. A suite of genome sequence based markers (DArTseq and Illumina Infinium SNPs) flanking the BnMn2+.A09 locus would provide an invaluable tool for various molecular breeding applications to improve canola production and profitability on Mn2+ toxic soils.
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Affiliation(s)
- Harsh Raman
- New South Wales Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
- *Correspondence: Harsh Raman,
| | - Rosy Raman
- New South Wales Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Brett McVittie
- New South Wales Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Beverley Orchard
- New South Wales Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Yu Qiu
- New South Wales Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Regine Delourme
- INRA, Agrocampus Ouest, Université de Rennes 1, UMR1349 Institut de Génétique, Environnement et de Protection des Plantes, Le Rheu, France
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Shi W, Hao C, Zhang Y, Cheng J, Zhang Z, Liu J, Yi X, Cheng X, Sun D, Xu Y, Zhang X, Cheng S, Guo P, Guo J. A Combined Association Mapping and Linkage Analysis of Kernel Number Per Spike in Common Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1412. [PMID: 28868056 PMCID: PMC5563363 DOI: 10.3389/fpls.2017.01412] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/31/2017] [Indexed: 05/18/2023]
Abstract
Kernel number per spike (KNPS) in wheat is a key factor that limits yield improvement. In this study, we genotyped a set of 264 cultivars, and a RIL population derived from the cross Yangmai 13/C615 using the 90 K wheat iSelect SNP array. We detected 62 significantly associated signals for KNPS at 47 single nucleotide polymorphism (SNP) loci through genome-wide association analysis of data obtained from multiple environments. These loci were on 19 chromosomes, and the phenotypic variation attributable to each one ranged from 1.53 to 39.52%. Twelve (25.53%) of the loci were also significantly associated with KNPS in the RIL population grown in multiple environments. For example, BS00022896_51-2ATT , BobWhite_c10539_201-2DAA , Excalibur_c73633_120-3BGG , and Kukri_c35508_426-7DTT were significantly associated with KNPS in all environments. Our findings demonstrate the effective integration of association mapping and linkage analysis for KNPS, and underpin KNPS as a target trait for marker-assisted selection and genetic fine mapping.
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Affiliation(s)
- Weiping Shi
- College of Agronomy, Shanxi Agricultural UniversityJinzhong, China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yong Zhang
- Key Laboratory of Wheat Biology and Genetic Improvement for Low and Middle Yangtze Valley (Ministry of Agriculture), Lixiahe Agricultural Institute of Jiangsu ProvinceYangzhou, China
| | - Jingye Cheng
- College of Agronomy, Yangzhou UniversityYangzhou, China
| | - Zheng Zhang
- College of Agronomy, Shanxi Agricultural UniversityJinzhong, China
| | - Jian Liu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low and Middle Yangtze Valley (Ministry of Agriculture), Lixiahe Agricultural Institute of Jiangsu ProvinceYangzhou, China
| | - Xin Yi
- Key Laboratory of Wheat Biology and Genetic Improvement for Low and Middle Yangtze Valley (Ministry of Agriculture), Lixiahe Agricultural Institute of Jiangsu ProvinceYangzhou, China
| | - Xiaoming Cheng
- Key Laboratory of Wheat Biology and Genetic Improvement for Low and Middle Yangtze Valley (Ministry of Agriculture), Lixiahe Agricultural Institute of Jiangsu ProvinceYangzhou, China
| | - Daizhen Sun
- College of Agronomy, Shanxi Agricultural UniversityJinzhong, China
| | - Yanhao Xu
- Hubei Collaborative Innovation Centre for Grain Industry and College of Agriculture, Yangtze UniversityJingzhou, China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Shunhe Cheng
- Key Laboratory of Wheat Biology and Genetic Improvement for Low and Middle Yangtze Valley (Ministry of Agriculture), Lixiahe Agricultural Institute of Jiangsu ProvinceYangzhou, China
- Shunhe Cheng
| | - Pingyi Guo
- College of Agronomy, Shanxi Agricultural UniversityJinzhong, China
- Pingyi Guo
| | - Jie Guo
- College of Agronomy, Shanxi Agricultural UniversityJinzhong, China
- *Correspondence: Jie Guo
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Wang H, Cheng H, Wang W, Liu J, Hao M, Mei D, Zhou R, Fu L, Hu Q. Identification of BnaYUCCA6 as a candidate gene for branch angle in Brassica napus by QTL-seq. Sci Rep 2016; 6:38493. [PMID: 27922076 PMCID: PMC5138835 DOI: 10.1038/srep38493] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 11/11/2016] [Indexed: 11/12/2022] Open
Abstract
Oilseed rape (Brassica napus L.) is one of the most important oil crops in China as well as worldwide. Branch angle as a plant architecture component trait plays an important role for high density planting and yield performance. In this study, bulked segregant analysis (BSA) combined with next generation sequencing technology was used to fine map QTL for branch angle. A major QTL, designated as branch angle 1 (ba1) was identified on A06 and further validated by Indel marker-based classical QTL mapping in an F2 population. Eighty-two genes were identified in the ba1 region. Among these genes, BnaA0639380D is a homolog of AtYUCCA6. Sequence comparison of BnaA0639380D from small- and big-branch angle oilseed rape lines identified six SNPs and four amino acid variation in the promoter and coding region, respectively. The expression level of BnaA0639380D is significantly higher in the small branch angle line Purler than in the big branch angle line Huyou19, suggesting that the genomic mutations may result in reduced activity of BnaA0639380D in Huyou19. Phytohormone determination showed that the IAA content in Purler was also obviously increased. Taken together, our results suggested BnaA0639380D is a possible candidate gene for branch angle in oilseed rape.
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Affiliation(s)
- Hui Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Hongtao Cheng
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Wenxiang Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Jia Liu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Mengyu Hao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Desheng Mei
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Rijin Zhou
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Li Fu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Qiong Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
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Bouchet AS, Laperche A, Bissuel-Belaygue C, Baron C, Morice J, Rousseau-Gueutin M, Dheu JE, George P, Pinochet X, Foubert T, Maes O, Dugué D, Guinot F, Nesi N. Genetic basis of nitrogen use efficiency and yield stability across environments in winter rapeseed. BMC Genet 2016; 17:131. [PMID: 27628849 PMCID: PMC5024496 DOI: 10.1186/s12863-016-0432-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/24/2016] [Indexed: 01/13/2023] Open
Abstract
Background Nitrogen use efficiency is an important breeding trait that can be modified to improve the sustainability of many crop species used in agriculture. Rapeseed is a major oil crop with low nitrogen use efficiency, making its production highly dependent on nitrogen input. This complex trait is suspected to be sensitive to genotype × environment interactions, especially genotype × nitrogen interactions. Therefore, phenotyping diverse rapeseed populations under a dense network of trials is a powerful approach to study nitrogen use efficiency in this crop. The present study aimed to determine the quantitative trait loci (QTL) associated with yield in winter oilseed rape and to assess the stability of these regions under contrasting nitrogen conditions for the purpose of increasing nitrogen use efficiency. Results Genome-wide association studies and linkage analyses were performed on two diversity sets and two doubled-haploid populations. These populations were densely genotyped, and yield-related traits were scored in a multi-environment design including seven French locations, six growing seasons (2009 to 2014) and two nitrogen nutrition levels (optimal versus limited). Very few genotype × nitrogen interactions were detected, and a large proportion of the QTL were stable across nitrogen nutrition conditions. In contrast, strong genotype × trial interactions in which most of the QTL were specific to a single trial were found. To obtain further insight into the QTL × environment interactions, genetic analyses of ecovalence were performed to identify the genomic regions contributing to the genotype × nitrogen and genotype × trial interactions. Fifty-one critical genomic regions contributing to the additive genetic control of yield-associated traits were identified, and the structural organization of these regions in the genome was investigated. Conclusions Our results demonstrated that the effect of the trial was greater than the effect of nitrogen nutrition levels on seed yield-related traits under our experimental conditions. Nevertheless, critical genomic regions associated with yield that were stable across environments were identified in rapeseed. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0432-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Anne Laperche
- AGROCAMPUS OUEST, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France.
| | | | - Cécile Baron
- INRA, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France
| | - Jérôme Morice
- INRA, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France
| | | | - Jean-Eric Dheu
- Limagrain Europe, Ferme de l'Etang, 77390, Verneuil-l'Etang, France
| | - Pierre George
- Biogemma, Chemin de Panedautes, 31700, Mondonville, France
| | - Xavier Pinochet
- Terres Inovia, Avenue Lucien Brétignières, 78850, Thiverval Grignon, France
| | - Thomas Foubert
- Euralis, Chemin de Panedautes, 31700, Mondonville, France
| | - Olivier Maes
- Maisadour Semences, Route de Saint Sever, BP27, 40001, Mont de Marsan Cedex, France
| | - Damien Dugué
- RAGT R2n, Rue Emile Singla, BP 3331, 12033, Rodez, France
| | - Florent Guinot
- Syngenta, Chemin de l'Hobit, 31790, Saint-Sauveur, France
| | - Nathalie Nesi
- INRA, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France
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Yang Y, Shi J, Wang X, Liu G, Wang H. Genetic architecture and mechanism of seed number per pod in rapeseed: elucidated through linkage and near-isogenic line analysis. Sci Rep 2016; 6:24124. [PMID: 27067010 PMCID: PMC4828700 DOI: 10.1038/srep24124] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/16/2016] [Indexed: 11/09/2022] Open
Abstract
Seed number per pod (SNPP) is one of the major yield components and breeding targets in rapeseed that shows great variation and is invaluable for genetic improvement. To elucidate the genetic architecture and uncover the mechanism of SNPP, we identified five quantitative trait loci (QTLs) using the BnaZNRIL population, which were integrated with those of previous studies by physical map to demonstrate a complex and relatively complete genetic architecture of SNPP. A major QTL, qSN.A6, was successfully fine-mapped from 1910 to 267 kb using near-isogenic line (NIL). In addition, qSN.A6 exhibited an antagonistic pleiotropy on seed weight (SW), which is caused by a physiological interaction in which SNPP acts "upstream" of SW. Because the negative effect of qSN.A6 on SW cannot fully counteract its positive effect on SNPP, it also enhanced the final yield (17.4%), indicating its great potential for utilization in breeding. The following genetic and cytological experiments further confirmed that the different rate of ovule abortion was responsible for the ~5 seed difference between Zhongshuang11 and NIL-qSN.A6. This systematic approach to dissecting the comprehensive genetic architecture of SNPP and characterizing the underlying mechanism has advanced the understanding of SNPP and will facilitate the development of high-yield cultivars.
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Affiliation(s)
- Yuhua Yang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Jiaqin Shi
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Guihua Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
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Wang X, Chen L, Wang A, Wang H, Tian J, Zhao X, Chao H, Zhao Y, Zhao W, Xiang J, Gan J, Li M. Quantitative trait loci analysis and genome-wide comparison for silique related traits in Brassica napus. BMC PLANT BIOLOGY 2016; 16:71. [PMID: 27000872 PMCID: PMC4802616 DOI: 10.1186/s12870-016-0759-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/15/2016] [Indexed: 05/02/2023]
Abstract
BACKGROUND Yield of rapeseed is determined by three components: silique number, seed number per silique and thousand seed weight. Seed number per silique and thousand seed weight are influenced by silique length, seed density, silique breadth, silique thickness and silique volume. Some QTLs for silique traits have been reported in B. napus, however, no studies have focused on the six agronomic traits (seed number per silique, silique length, silique breadth, silique thickness, seed density and silique volume) simultaneously, and the genetic determinism of such complex traits have not been fully elucidated. RESULTS In this study, the six silique traits were evaluated using 348 lines of a doubled haploid population, the KN population. The results showed that 2, 4, 1, 1 and 2 QTLs explaining > 10 % of phenotypic variation were obtained for silique length, silique breadth, silique thickness, seed number per silique and silique volume, respectively. Notably, three major effect QTLs (cqSB-C6-1, cqSB-C6-2 and cqSV-C6-3) were identified in at least three environments, and 17 unique QTLs controlling at least two traits were obtained. A high-density consensus map containing 1225 markers was constructed for QTL comparison by combining the KN map with other five published maps. The comparative results revealed that 14, 13 and 11 QTLs for silique breadth, silique thickness and silique volume might be the potential new QTLs because few QTLs for these traits were reported in B. napus. In addition, potential new QTLs for silique length (11), seed number per silique (6) and seed density (5) were also identified. Twenty-five candidate genes underlying 27 QTLs for silique related traits were obtained. CONCLUSIONS This study constructed QTL analysis in B. napus, and obtained 60 consensus QTLs for six silique related traits. The potential new QTLs will enhance our understanding of the genetic control of silique traits, and the stable QTLs provided the targets for improving seed yield in future. These findings provided comprehensive insights into the genetic network affecting silique traits at QTL level in B. napus.
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Affiliation(s)
- Xiaodong Wang
- />Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China
- />Provincial Key Laboratory of Agrobiology, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Li Chen
- />Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China
- />Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000 China
| | - Aina Wang
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Hao Wang
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Jianhua Tian
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Xiaoping Zhao
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Hongbo Chao
- />Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China
| | - Yajun Zhao
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Weiguo Zhao
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Jun Xiang
- />Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000 China
| | - Jianping Gan
- />Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000 China
| | - Maoteng Li
- />Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China
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Rapid Identification of Candidate Genes for Seed Weight Using the SLAF-Seq Method in Brassica napus. PLoS One 2016; 11:e0147580. [PMID: 26824525 PMCID: PMC4732658 DOI: 10.1371/journal.pone.0147580] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/04/2016] [Indexed: 11/30/2022] Open
Abstract
Seed weight is a critical and direct trait for oilseed crop seed yield. Understanding its genetic mechanism is of great importance for yield improvement in Brassica napus breeding. Two hundred and fifty doubled haploid lines derived by microspore culture were developed from a cross between a large-seed line G-42 and a small-seed line 7–9. According to the 1000-seed weight (TSW) data, the individual DNA of the heaviest 46 lines and the lightest 47 lines were respectively selected to establish two bulked DNA pools. A new high-throughput sequencing technology, Specific Locus Amplified Fragment Sequencing (SLAF-seq), was used to identify candidate genes of TSW in association analysis combined with bulked segregant analysis (BSA). A total of 1,933 high quality polymorphic SLAF markers were developed and 4 associated markers of TSW were procured. A hot region of ~0.58 Mb at nucleotides 25,401,885–25,985,931 on ChrA09 containing 91 candidate genes was identified as tightly associated with the TSW trait. From annotation information, four genes (GSBRNA2T00037136001, GSBRNA2T00037157001, GSBRNA2T00037129001 and GSBRNA2T00069389001) might be interesting candidate genes that are highly related to seed weight.
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Kim S, Welsh DA, Myers L, Cherry KE, Wyckoff J, Jazwinski SM. Non-coding genomic regions possessing enhancer and silencer potential are associated with healthy aging and exceptional survival. Oncotarget 2016; 6:3600-12. [PMID: 25682868 PMCID: PMC4414140 DOI: 10.18632/oncotarget.2877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 12/08/2014] [Indexed: 01/04/2023] Open
Abstract
We have completed a genome-wide linkage scan for healthy aging using data collected from a family study, followed by fine-mapping by association in a separate population, the first such attempt reported. The family cohort consisted of parents of age 90 or above and their children ranging in age from 50 to 80. As a quantitative measure of healthy aging, we used a frailty index, called FI34, based on 34 health and function variables. The linkage scan found a single significant linkage peak on chromosome 12. Using an independent cohort of unrelated nonagenarians, we carried out a fine-scale association mapping of the region suggestive of linkage and identified three sites associated with healthy aging. These healthy-aging sites (HASs) are located in intergenic regions at 12q13-14. HAS-1 has been previously associated with multiple diseases, and an enhancer was recently mapped and experimentally validated within the site. HAS-2 is a previously uncharacterized site possessing genomic features suggestive of enhancer activity. HAS-3 contains features associated with Polycomb repression. The HASs also contain variants associated with exceptional longevity, based on a separate analysis. Our results provide insight into functional genomic networks involving non-coding regulatory elements that are involved in healthy aging and longevity.
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Affiliation(s)
- Sangkyu Kim
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - David A Welsh
- Department of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Leann Myers
- Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Katie E Cherry
- Department of Psychology, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jennifer Wyckoff
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - S Michal Jazwinski
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
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Dun X, Tao Z, Wang J, Wang X, Liu G, Wang H. Comparative Transcriptome Analysis of Primary Roots of Brassica napus Seedlings with Extremely Different Primary Root Lengths Using RNA Sequencing. FRONTIERS IN PLANT SCIENCE 2016; 7:1238. [PMID: 27594860 PMCID: PMC4990598 DOI: 10.3389/fpls.2016.01238] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/04/2016] [Indexed: 05/18/2023]
Abstract
Primary root (PR) development is a crucial developmental process that is essential for plant survival. The elucidation of the PR transcriptome provides insight into the genetic mechanism controlling PR development in crops. In this study, we performed a comparative transcriptome analysis to investigate the genome-wide gene expression profiles of the seedling PRs of four Brassica napus genotypes that were divided into two groups, short group (D43 and D61), and long group (D69 and D72), according to their extremely different primary root lengths (PRLs). The results generated 55,341,366-64,631,336 clean reads aligned to 62,562 genes (61.9% of the current annotated genes) in the B. napus genome. We provide evidence that at least 44,986 genes are actively expressed in the B. napus PR. The majority of the genes that were expressed during seedling PR development were associated with metabolism, cellular processes, response to stimulus, biological regulation, and signaling. Using a pairwise comparison approach, 509 differentially expressed genes (DEGs; absolute value of log2 fold-change ≥1 and p ≤ 0.05) between the long and short groups were revealed, including phytohormone-related genes, protein kinases and phosphatases, oxygenase, cytochrome P450 proteins, etc. Combining GO functional category, KEGG, and MapMan pathway analyses indicated that the DEGs involved in cell wall metabolism, carbohydrate metabolism, lipid metabolism, secondary metabolism, protein modification and degradation, hormone pathways and signaling pathways were the main causes of the observed PRL differences. We also identified 16 differentially expressed transcription factors (TFs) involved in PR development. Taken together, these transcriptomic datasets may serve as a foundation for the identification of candidate genes and may provide valuable information for understanding the molecular and cellular events related to PR development.
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Liu J, Wang J, Wang H, Wang W, Zhou R, Mei D, Cheng H, Yang J, Raman H, Hu Q. Multigenic Control of Pod Shattering Resistance in Chinese Rapeseed Germplasm Revealed by Genome-Wide Association and Linkage Analyses. FRONTIERS IN PLANT SCIENCE 2016; 7:1058. [PMID: 27493651 PMCID: PMC4954820 DOI: 10.3389/fpls.2016.01058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 07/06/2016] [Indexed: 05/03/2023]
Abstract
The majority of rapeseed cultivars shatter seeds upon maturity especially under hot-dry and windy conditions, reducing yield and gross margin return to growers. Here, we identified quantitative trait loci (QTL) for resistance to pod shatter in an unstructured diverse panel of 143 rapeseed accessions, and two structured populations derived from bi-parental doubled haploid (DH) and inter-mated (IF2) crosses derived from R1 (resistant to pod shattering) and R2 (prone to pod shattering) accessions. Genome-wide association analysis identified six significant QTL for resistance to pod shatter located on chromosomes A01, A06, A07, A09, C02, and C05. Two of the QTL, qSRI.A09 delimited with the SNP marker Bn-A09-p30171993 (A09) and qSRI.A06 delimited with the SNP marker Bn-A06-p115948 (A06) could be repeatedly detected across environments in a diversity panel, DH and IF2 populations, suggesting that at least two loci on chromosomes A06 and A09 were the main contributors to pod shatter resistance in Chinese germplasm. Significant SNP markers identified in this study especially those that appeared repeatedly across environments provide a cost-effective and an efficient method for introgression and pyramiding of favorable alleles for pod shatter resistance via marker-assisted selection in rapeseed improvement programs.
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Affiliation(s)
- Jia Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Jun Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
- Graduate School of Chinese Academy of Agricultural SciencesBeijing, China
| | - Hui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Wenxiang Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Rijin Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Desheng Mei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Hongtao Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Juan Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Harsh Raman
- Graham Centre for Agricultural Innovation (an Alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural InstituteWagga Wagga, NSW, Australia
- *Correspondence: Harsh Raman
| | - Qiong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
- Qiong Hu
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