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Tian Z, Wang X, Dun X, Zhao K, Wang H, Ren L. An integrated QTL mapping and transcriptome sequencing provides further molecular insights and candidate genes for stem strength in rapeseed (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:38. [PMID: 38294547 DOI: 10.1007/s00122-023-04535-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024]
Abstract
KEY MESSAGE We detected the major QTL- qSR.A07, which regulated stem strength and was fine-mapped to 490 kb. BnaA07G0302800ZS and BnaA07G0305700ZS as the candidate functional genes were identified at qSR.A07 locus. The stem's mechanical properties reflect its ability to resist lodging. In rapeseed (Brassica napus L.), although stem lodging negatively affects yield and generates harvesting difficulties, the molecular regulation of stem strength remains elusive. Hence, this study aimed to unravel the main loci and molecular mechanisms governing rapeseed stem strength. A mapping population consisting of 267 RILs (recombinant inbred lines) was developed from the crossed between ZS11 (high stem strength) and 4D122 (low stem strength), and two mechanical properties of stems including stem breaking strength and stem rind penetrometer resistance were phenotyped in four different environments. Four pleiotropic QTLs that were stable in at least two environments were detected. qSR.A07, the major one, was fine-mapped to a 490 kb interval between markers SA7-2711 and SA7-2760 on chromosome 7. It displayed epistatic interaction with qRPR.A09-2. Comparative transcriptome sequencing and analysis unveiled methionine/S-adenosylmethionine cycle (Met/SAM cycle), cytoskeleton organization, sulfur metabolism and phenylpropanoid biosynthesis as the main pathways associated with high stem strength. Further, we identified two candidate genes, BnaA07G0302800ZS and BnaA07G0305700ZS, at qSR.A07 locus. Gene sequence alignment identified a number of InDels, SNPs and amino acid variants in sequences of these genes between ZS11 and 4D122. Finally, based on these genetic variants, we developed three SNP markers of these genes to facilitate future genetic selection and functional studies. These findings offer important genetic resources for the molecular-assisted breeding of novel rapeseed stem lodging-resistant varieties.
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Affiliation(s)
- Zhengshu Tian
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Industrial Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaoling Dun
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Kaiqin Zhao
- Industrial Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
| | - Lijun Ren
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'An, China.
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Zhao K, Dong J, Xu J, Bai Y, Yin Y, Long C, Wu L, Lin T, Fan L, Wang Y, Edger PP, Xiong Z. Downregulation of the expression of subgenomic chromosome A7 genes promotes plant height in resynthesized allopolyploid Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:11. [PMID: 38110525 DOI: 10.1007/s00122-023-04510-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/18/2023] [Indexed: 12/20/2023]
Abstract
KEY MESSAGE Homoeolog expression bias and the gene dosage effect induce downregulation of genes on chromosome A7, causing a significant increase in the plant height of resynthesized allopolyploid Brassica napus. Gene expression levels in allopolyploid plants are not equivalent to the simple average of the expression levels in the parents and are associated with several non-additive expression phenomena, including homoeolog expression bias. However, hardly any information is available on the effect of homoeolog expression bias on traits. Here, we studied the effects of gene expression-related characteristics on agronomic traits using six isogenic resynthesized Brassica napus lines across the first ten generations. We found a group of genes located on chromosome A7 whose expression levels were significantly negatively correlated with plant height. They were expressed at significantly lower levels than their homoeologous genes, owing to allopolyploidy rather than inheritance from parents. Homoeolog expression bias resulted in resynthesized allopolyploids with a plant height similar to their female Brassica oleracea parent, but significantly higher than that of the male Brassica rapa parent. Notably, aneuploid lines carrying monosomic and trisomic chromosome A7 had the highest and lowest plant heights, respectively, due to changes in the expression bias of homoeologous genes because of alterations in the gene dosage. These findings suggest that the downregulation of the expression of homoeologous genes on a single chromosome can result in the partial improvement of traits to a significant extent in the nascent allopolyploid B. napus.
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Affiliation(s)
- Kanglu Zhao
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Jing Dong
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Junxiong Xu
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yanbo Bai
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yuhe Yin
- Institute of Ulanqab Agricultural and Forestry Sciences, Ulanqab, 012000, Inner Mongolia, China
| | - Chunshen Long
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Lei Wu
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Tuanrong Lin
- Institute of Ulanqab Agricultural and Forestry Sciences, Ulanqab, 012000, Inner Mongolia, China
| | - Longqiu Fan
- Institute of Ulanqab Agricultural and Forestry Sciences, Ulanqab, 012000, Inner Mongolia, China
| | - Yufeng Wang
- Institute of Ulanqab Agricultural and Forestry Sciences, Ulanqab, 012000, Inner Mongolia, China
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA.
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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Ding T, Cai L, He Y, Li Y, Tian E, Zhou Q, Zhou X, Wang X, Yu K, Shen X. BnPLP1 Positively Regulates Flowering Time, Plant Height, and Main Inflorescence Length in Brassica napus. Genes (Basel) 2023; 14:2206. [PMID: 38137028 PMCID: PMC10743044 DOI: 10.3390/genes14122206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Protein prenylation mediated by the Arabidopsis thaliana PLURIPETALA (AtPLP) gene plays a crucial role in plant growth, development, and environmental response by adding a 15-carbon farnesyl group or one to two 20-carbon geranylgeranyl groups onto one to two cysteine residues at the C-terminus of the target protein. However, the homologous genes and their functions of AtPLP in rapeseed are unclear. In this study, bioinformatics analysis and gene cloning demonstrated the existence of two homologous genes of AtPLP in the Brassica napus L. genome, namely, BnPLP1 and BnPLP2. Evolutionary analysis revealed that BnPLP1 originated from the B. rapa L. genome, while BnPLP2 originated from the B. oleracea L. genome. Genetic transformation analysis revealed that the overexpression of BnPLP1 in Arabidopsis plants exhibited earlier flowering initiation, a prolonged flowering period, increased plant height, and longer main inflorescence length compared to the wild type. Contrarily, the downregulation of BnPLP1 expression in B. napus plants led to delayed flowering initiation, shortened flowering period, decreased plant height, and reduced main inflorescence length compared to the wild type. These findings indicate that the BnPLP1 gene positively regulates flowering time, plant height, and main inflorescence length. This provides a new gene for the genetic improvement of flowering time and plant architecture in rapeseed.
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Affiliation(s)
- Ting Ding
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Lei Cai
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
- Center for Research and Development of Fine Chemical of Guizhou University, Guiyang 550025, China
| | - Yuqi He
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Yuanhong Li
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Entang Tian
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Qianhui Zhou
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Xufan Zhou
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Xiaodong Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China;
| | - Kunjiang Yu
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
- Center for Research and Development of Fine Chemical of Guizhou University, Guiyang 550025, China
| | - Xinjie Shen
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
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Ting NC, Chan PL, Buntjer J, Ordway JM, Wischmeyer C, Ooi LCL, Low ETL, Marjuni M, Sambanthamurthi R, Singh R. High-resolution genetic linkage map and height-related QTLs in an oil palm ( Elaeis guineensis) family planted across multiple sites. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1301-1318. [PMID: 38024957 PMCID: PMC10678900 DOI: 10.1007/s12298-023-01360-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 09/09/2023] [Accepted: 09/14/2023] [Indexed: 12/01/2023]
Abstract
A refined SNP array containing 92,459 probes was developed and applied for chromosome scanning, construction of a high-density genetic linkage map and QTL analysis in a selfed Nigerian oil palm family (T128). Genotyping of the T128 mapping family generated 76,447 good quality SNPs for detailed scanning of aberration and homozygosity in the individual pseudo-chromosomes. Of them, 25,364 polymorphic SNPs were used for linkage analysis resulting in an 84.4% mapping rate. A total of 21,413 SNPs were mapped into 16 linkage groups (LGs), covering a total map length of 1364.5 cM. This genetic map is 16X denser than the previous version used to establish pseudo-chromosomes of the oil palm reference genome published in 2013. The QTLs associated with height, height increment and rachis length were identified in LGs TT05, 06, 08, 15 and 16. The present QTLs as well as those published previously were tagged to the reference genome to determine their chromosomal locations. Almost all the QTLs identified in this study were either close to or co-located with those reported in other populations. Determining the QTL position on chromosomes was also helpful in mining for the underlying candidate genes. In total, 55 putative genes and transcription factors involved in the biosynthesis, conjugation and signalling of the major phytohormones, especially for gibberellins and cell wall morphogenesis were found to be present in the identified genomic QTL regions, and their potential roles in plant dwarfism are discussed. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01360-2.
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Affiliation(s)
- Ngoot-Chin Ting
- Malaysian Palm Oil Board (MPOB), Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Pek-Lan Chan
- Malaysian Palm Oil Board (MPOB), Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | | | | | | | - Leslie Cheng-Li Ooi
- Malaysian Palm Oil Board (MPOB), Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Eng Ti Leslie Low
- Malaysian Palm Oil Board (MPOB), Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Marhalil Marjuni
- Malaysian Palm Oil Board (MPOB), Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Ravigadevi Sambanthamurthi
- Malaysian Palm Oil Board (MPOB), Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Rajinder Singh
- Malaysian Palm Oil Board (MPOB), Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
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Zhang Y, Zhang Q, Wang H, Tao S, Cao H, Shi Y, Bakirov A, Xu A, Huang Z. Discovery of common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits in Brassica napus L. PLANT CELL REPORTS 2023; 42:1039-1057. [PMID: 37076701 DOI: 10.1007/s00299-023-03011-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits were identified in Brassica napus combining QTL mapping with transcriptome under salt and alkaline stresses. The yield of rapeseed (Brassica napus L.) is determined by multiple yield-related traits, which are susceptible to environmental factors. Many yield-related quantitative trait loci (QTLs) have been reported in Brassica napus; however, no studies have been conducted to investigate both salt-alkali tolerance and yield-related traits simultaneously. Here, specific-locus amplified fragment sequencing (SLAF-seq) technologies were utilized to map the QTLs for salt-alkali tolerance and yield-related traits. A total of 65 QTLs were identified, including 30 QTLs for salt-alkali tolerance traits and 35 QTLs for yield-related traits, accounting for 7.61-27.84% of the total phenotypic variations. Among these QTLs, 18 unique QTLs controlling two to four traits were identified by meta-analysis. Six novel and unique QTLs were detected for salt-alkali tolerance traits. By comparing these unique QTLs for salt-alkali tolerance traits with those previously reported QTLs for yield-related traits, seven co-localized chromosomal regions were identified on A09 and A10. Combining QTL mapping with transcriptome of two parents under salt and alkaline stresses, thirteen genes were identified as the candidates controlling both salt-alkali tolerance and yield. These findings provide useful information for future breeding of high-yield cultivars resistant to alkaline and salt stresses.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qi Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Han Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shunxian Tao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hanming Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yiji Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Aldiyar Bakirov
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Aixia Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Mathur S, Singh P, Yadava SK, Gupta V, Pradhan AK, Pental D. Genetic mapping of some key plant architecture traits in Brassica juncea using a doubled haploid population derived from a cross between two distinct lines: vegetable type Tumida and oleiferous Varuna. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:96. [PMID: 37017803 DOI: 10.1007/s00122-023-04321-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 02/09/2023] [Indexed: 06/19/2023]
Abstract
Genetic mapping of some key plant architectural traits in a vegetable type and an oleiferous B. juncea cross revealed QTL and candidate genes for breeding more productive ideotypes. Brassica juncea (AABB, 2n = 36), commonly called mustard, is an allopolyploid crop of recent origin but contains considerable morphological and genetic variation. An F1-derived doubled haploid population developed from a cross between an Indian oleiferous line, Varuna, and a Chinese stem type vegetable mustard, Tumida showed significant variability for some key plant architectural traits-four stem strength-related traits, stem diameter (Dia), plant height (Plht), branch initiation height (Bih), number of primary branches (Pbr), and days to flowering (Df). Multi-environment QTL analysis identified twenty Stable QTL for the above-mentioned nine plant architectural traits. Though Tumida is ill-adapted to the Indian growing conditions, it was found to contribute favorable alleles in Stable QTL for five architectural traits-press force, Dia, Plht, Bih, and Pbr; these QTL could be used to breed superior ideotypes in the oleiferous mustard lines. A QTL cluster on LG A10 contained Stable QTL for seven architectural traits that included major QTL (phenotypic variance ≥ 10%) for Df and Pbr, with Tumida contributing the trait-enhancing alleles for both. Since early flowering is critical for the cultivation of mustard in the Indian subcontinent, this QTL cannot be used for the improvement of Pbr in the Indian gene pool lines. Conditional QTL analysis for Pbr, however, identified other QTL which could be used for the improvement of Pbr without affecting Df. The Stable QTL intervals were mapped on the genome assemblies of Tumida and Varuna for the identification of candidate genes.
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Affiliation(s)
- Shikha Mathur
- Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India
| | - Priyansha Singh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Satish Kumar Yadava
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Vibha Gupta
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Akshay Kumar Pradhan
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India.
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Dong Z, Tang M, Cui X, Zhao C, Tong C, Liu Y, Xiang Y, Li Z, Huang J, Cheng X, Liu S. Integrating GWAS, linkage mapping and gene expression analyses reveal the genetic control of first branch height in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2022; 13:1080999. [PMID: 36589070 PMCID: PMC9798901 DOI: 10.3389/fpls.2022.1080999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Rapeseed (Brassica napus L.) is a crucial oil crop cultivated worldwide. First branch height, an essential component of rapeseed plant architecture, has an important effect on yield and mechanized harvesting; however, the underlying genetic mechanism remains unclear. In this study, based on the 60K single nucleotide polymorphism array and a recombinant inbred lines population derived from M083 and 888-5, a total of 19 QTLs were detected in five environments, distributed on linkage groups A02, A09, A10, C06, and C07, which explained phenotypic variation ranging from 4.87 to 29.87%. Furthermore, 26 significant SNPs were discovered on Chr.A02 by genome-wide association study in a diversity panel of 324 re-sequencing accessions. The major QTL of the first branch height trait was co-located on Chr.A02 by integrating linkage mapping and association mapping. Eleven candidate genes were screened via allelic variation analysis, inter-subgenomic synteny analysis, and differential expression of genes in parental shoot apical meristem tissues. Among these genes, BnaA02g13010D, which encodes a TCP transcription factor, was confirmed as the target gene according to gene function annotation, haplotype analysis, and full-length gene sequencing, which revealed that TATA insertion/deletion in the promoter region was closely linked to significantly phenotypic differences BnaA02.TCP1 M083 overexpression resulted in decreased branch height and increased branch number in Arabidopsis. These results provide a genetic basis for first branch height and the ideal architecture of B. napus.
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Affiliation(s)
- Zhixue Dong
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Minqiang Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, School of Forestry, Hainan University, Haikou, China
| | - Xiaobo Cui
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chuanji Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yueying Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Science, Guiyang, China
| | - Zaiyun Li
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junyan Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaohui Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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Han X, Tang Q, Xu L, Guan Z, Tu J, Yi B, Liu K, Yao X, Lu S, Guo L. Genome-wide detection of genotype environment interactions for flowering time in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:1065766. [PMID: 36479520 PMCID: PMC9721451 DOI: 10.3389/fpls.2022.1065766] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
Flowering time is strongly related to the environment, while the genotype-by-environment interaction study for flowering time is lacking in Brassica napus. Here, a total of 11,700,689 single nucleotide polymorphisms in 490 B. napus accessions were used to associate with the flowering time and related climatic index in eight environments using a compressed variance-component mixed model, 3VmrMLM. As a result, 19 stable main-effect quantitative trait nucleotides (QTNs) and 32 QTN-by-environment interactions (QEIs) for flowering time were detected. Four windows of daily average temperature and precipitation were found to be climatic factors highly correlated with flowering time. Ten main-effect QTNs were found to be associated with these flowering-time-related climatic indexes. Using differentially expressed gene (DEG) analysis in semi-winter and spring oilseed rapes, 5,850 and 5,511 DEGs were found to be significantly expressed before and after vernalization. Twelve and 14 DEGs, including 7 and 9 known homologs in Arabidopsis, were found to be candidate genes for stable QTNs and QEIs for flowering time, respectively. Five DEGs were found to be candidate genes for main-effect QTNs for flowering-time-related climatic index. These candidate genes, such as BnaFLCs, BnaFTs, BnaA02.VIN3, and BnaC09.PRR7, were further validated by the haplotype, selective sweep, and co-expression networks analysis. The candidate genes identified in this study will be helpful to breed B. napus varieties adapted to particular environments with optimized flowering time.
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Affiliation(s)
- Xu Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Qingqing Tang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Liping Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Zhilin Guan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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9
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Jiao Y, Liang B, Yang G, Xin Q, Hong D. A simple and efficient method to quantify the cell parameters of the seed coat, embryo and silique wall in rapeseed. PLANT METHODS 2022; 18:117. [PMID: 36329545 PMCID: PMC9632141 DOI: 10.1186/s13007-022-00948-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Researchers interested in the seed size of rapeseed need to quantify the cell size and number of cells in the seed coat, embryo and silique wall. Scanning electron microscope-based methods have been demonstrated to be feasible but laborious and costly. After image preparation, the cell parameters are generally evaluated manually, which is time consuming and a major bottleneck for large-scale analysis. Recently, two machine learning-based algorithms, Trainable Weka Segmentation (TWS) and Cellpose, were released to overcome this long-standing problem. Moreover, the MorphoLibJ and LabelsToROIs plugins in Fiji provide user-friendly tools to deal with cell segmentation files. We attempted to verify the practicability and efficiency of these advanced tools for various types of cells in rapeseed. RESULTS We simplified the current image preparation procedure by skipping the fixation step and demonstrated the feasibility of the simplified procedure. We developed three methods to automatically process multicellular images of various tissues in rapeseed. The TWS-Fiji (TF) method combines cell detection with TWS and cell measurement with Fiji, enabling the accurate quantification of seed coat cells. The Cellpose-Fiji (CF) method, based on cell segmentation with Cellpose and quantification with Fiji, achieves good performance but exhibits systematic error. By removing border labels with MorphoLibJ and detecting regions of interest (ROIs) with LabelsToROIs, the Cellpose-MorphoLibJ-LabelsToROIs (CML) method achieves human-level performance on bright-field images of seed coat cells. Intriguingly, the CML method needs very little manual calibration, a property that makes it suitable for massive-scale image processing. Through a large-scale quantitative evaluation of seed coat cells, we demonstrated the robustness and high efficiency of the CML method at both the single-cell level and the sample level. Furthermore, we extended the application of the CML method to developing seed coat, embryo and silique wall cells and acquired highly precise and reliable results, indicating the versatility of this method for use in multiple scenarios. CONCLUSIONS The CML method is highly accurate and free of the need for manual correction. Hence, it can be applied for the low-cost, high-throughput quantification of diverse cell types in rapeseed with high efficiency. We envision that this method will facilitate the functional genomics and microphenomics studies of rapeseed and other crops.
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Affiliation(s)
- Yushun Jiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Baoling Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Qiang Xin
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
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10
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Ren R, Liu W, Yao M, Jia Y, Huang L, Li W, He X, Guan M, Liu Z, Guan C, Hua W, Xiong X, Qian L. Regional association and transcriptome analysis revealed candidate genes controlling plant height in Brassica napus. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:69. [PMID: 37313473 PMCID: PMC10248621 DOI: 10.1007/s11032-022-01337-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/07/2022] [Indexed: 06/15/2023]
Abstract
Plant height is a key morphological trait in rapeseed, which not only plays an important role in determining plant architecture, but is also an important characteristic related to yield. Presently, the improvement of plant architecture is a major challenge in rapeseed breeding. This work was carried out to identify genetic loci related to plant height in rapeseed. In this study, a genome-wide association study (GWAS) of plant height was performed using a Brassica 60 K Illumina Infinium SNP array and 203 Brassica napus accessions. Eleven haplotypes containing important candidate genes were detected and significantly associated with plant height on chromosomes A02, A03, A05, A07, A08, C03, C06, and C09. Moreover, regional association analysis of 50 resequenced rapeseed inbred lines was used to further analyze these eleven haplotypes and revealed nucleotide variation in the BnFBR12-A08 and BnCCR1-C03 gene regions related to the phenotypic variation in plant height. Furthermore, coexpression network analysis showed that BnFBR12-A08 and BnCCR1-C03 were directly connected with hormone genes and transcription factors and formed a potential network regulating the plant height of rapeseed. Our results will aid in the development of haplotype functional markers to further improve plant height in rapeseed. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01337-1.
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Affiliation(s)
- Rui Ren
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Wei Liu
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Min Yao
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Yuan Jia
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Luyao Huang
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Wenqian Li
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Xin He
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Mei Guan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Zhongsong Liu
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Chunyun Guan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Wei Hua
- 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
| | - Xinghua Xiong
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Lunwen Qian
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
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11
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Jin Q, Gao G, Guo C, Yang T, Li G, Song J, Zheng N, Yin S, Yi L, Li Z, Ge X, King GJ, Wang J, Zhou G. Transposon insertions within alleles of BnaFT.A2 are associated with seasonal crop type in rapeseed. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3469-3483. [PMID: 35997786 DOI: 10.1007/s00122-022-04193-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
We identified two new transposon insertions within the promoter of BnaFT.A2 in addition to an existing 288 bp MITE within the second intron. Each insertion event corresponds to a distinct BnaFT.A2 haplotype and is closely associated with established crop seasonal ecotypes. Florigen, encoded by FLOWERING LOCUS T (FT), plays key roles not only as a flowering hormone, but also a universal growth factor affecting several aspects of plant architecture. In rapeseed, BnaFT.A2 has been revealed as one of the major loci associated with flowering time and different ecotypes. However, it is unclear how allelic variations of BnaFT.A2 affect its function in flowering time regulation and beyond. In this study, we confirmed an existing 288 bp miniature inverted-repeat transposable element (MITE) insertion within the second intron and identified two new insertions within the promoter of BnaFT.A2-a 3971 bp CACTA and a 1079 bp Helitron. Each insertion event corresponds to a distinct BnaFT.A2 haplotype and is closely associated with established crop seasonal ecotypes. These alleles have similar tissue-specific expression patterns but discrete transcriptional patterns tightly associated with rapeseed flowering time and ecotype. RNAi lines and mutants of BnaFT.A2 flowered significantly later than controls. Differentially expressed genes (DEGs), identified in transcriptomic profiling of seedling leaves from two loss-of-function mutants (Bnaft.a2-L1 and Bnaft.a2-L2) compared with controls, indicated significant enrichment for hormone metabolic genes and roles related to plant cell wall synthesis and photosynthesis. Plants with loss-of-function BnaFT.A2 had smaller leaves and lower net photosynthetic rate compared to controls. These findings not only further clarify the genetic basis of flowering time variation and ecotype formation in B. napus, but also provide an additional toolbox for genetic improvement of seasonal adaptation and production.
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Affiliation(s)
- Qingdong Jin
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gengdong Gao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaocheng Guo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Taihua Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ge Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jurong Song
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Na Zheng
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuai Yin
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Licong Yi
- Cash Crops Institute, Hubei Academy of Agricultural Science, Wuhan, 430064, China
| | - Zhen Li
- School of Agriculture, Jinhua Polytechnic, Jinhua, 321007, China
| | - Xianhong Ge
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Jing Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Guangsheng Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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12
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Prapas D, Scalone R, Lee J, Nurkowski KA, Bou‐assi S, Rieseberg L, Battlay P, Hodgins KA. Quantitative trait loci mapping reveals an oligogenic architecture of a rapidly adapting trait during the European invasion of common ragweed. Evol Appl 2022; 15:1249-1263. [PMID: 36051461 PMCID: PMC9423086 DOI: 10.1111/eva.13453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/05/2022] [Accepted: 06/30/2022] [Indexed: 01/09/2023] Open
Abstract
Biological invasions offer a unique opportunity to investigate evolution over contemporary timescales. Rapid adaptation to local climates during range expansion can be a major determinant of invasion success, yet fundamental questions remain about its genetic basis. This study sought to investigate the genetic basis of climate adaptation in invasive common ragweed (Ambrosia artemisiifolia). Flowering time adaptation is key to this annual species' invasion success, so much so that it has evolved repeated latitudinal clines in size and phenology across its native and introduced ranges despite high gene flow among populations. Here, we produced a high-density linkage map (4493 SNPs) and paired this with phenotypic data from an F2 mapping population (n = 336) to identify one major and two minor quantitative trait loci (QTL) underlying flowering time and height differentiation in this species. Within each QTL interval, several candidate flowering time genes were also identified. Notably, the major flowering time QTL detected in this study was found to overlap with a previously identified haploblock (putative inversion). Multiple genetic maps of this region identified evidence of suppressed recombination in specific genotypes, consistent with inversions. These discoveries support the expectation that a concentrated genetic architecture with fewer, larger, and more tightly linked alleles should underlie rapid local adaptation during invasion, particularly when divergently adapting populations experience high levels of gene flow.
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Affiliation(s)
- Diana Prapas
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Romain Scalone
- Department of Crop Production Ecology, Uppsala Ecology CenterSwedish University of Agricultural SciencesUppsalaSweden,Department of Grapevine BreedingHochschule Geisenheim UniversityGeisenheimGermany
| | - Jacqueline Lee
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Kristin A. Nurkowski
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia,Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverCanada
| | - Sarah Bou‐assi
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Loren Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverCanada
| | - Paul Battlay
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Kathryn A. Hodgins
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
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13
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Zhang S, Liu W, Cheng X, Wang Z, Yuan F, Wu W, Liao S. Evaluating the productivity of ancient Pu'er tea trees (Camellia sinensis var. assamica): a multivariate modeling approach. PLANT METHODS 2022; 18:95. [PMID: 35897068 PMCID: PMC9327265 DOI: 10.1186/s13007-022-00928-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The demand for productive economic plant resources is increasing with the continued growth of the human population. Ancient Pu'er tea trees [Camellia sinensis var. assamica (J. W. Mast.) Kitam.] are an important ecological resource with high economic value and large interests. The study intends to explore and evaluate critical drivers affecting the species' productivity, then builds formulas and indexes to make predicting the productivity of such valuable plant resources possible and applicable. RESULTS Our analysis identified the ideal values of the seven most important environmental variables and their relative contribution (shown in parentheses) to the distribution of ancient Pu'er tea trees: annual precipitation, ca. 1245 mm (28.73%); min temperature of coldest month, ca. 4.2 °C (18.25%); precipitation of driest quarter, ca. 47.5 mm (14.45%); isothermality, 49.9% to 50.4% (14.11%); precipitation seasonality, ca. 89.2 (6.77%); temperature seasonality, ca. 391 (4.46%); and solar radiation, 12,250 to 13,250 kJ m-2 day-1 (3.28%). Productivity was indicated by the total value (viz. fresh leaf harvested multiplied by unit price) of each tree. Environmental suitability, tree growth, and management positively affected productivity; regression weights were 0.325, 0.982, and 0.075, respectively. The degree of productivity was classified as follows: > 0.8, "highly productive"; 0.5-0.8, "productive"; 0.3-0.5, "poorly productive"; and < 0.3, "unproductive". Overall, 53% of the samples were categorized as "poorly productive" or "unproductive"; thus, the management of these regions require attention. CONCLUSIONS This model improves the accuracy of the predictions of ancient Pu'er tea tree productivity and will aid future analyses of distribution shifts under climate change, as well as the identification of areas suitable for Pu'er tea tree plantations. Our modeling framework provides insights that facilitate the interpretation of abstract concepts and could be applied to other economically valuable plant resources.
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Affiliation(s)
- Shuqiao Zhang
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650216, Yunnan, China.
- Fenner School of Environment & Society, College of Science, Australian National University, Canberra, ACT, 2601, Australia.
| | - Wendou Liu
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650216, Yunnan, China
| | - Xinmeng Cheng
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650216, Yunnan, China
| | - Zizhi Wang
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650216, Yunnan, China
| | - Fengjun Yuan
- Yunnan Institute of Forest Inventory and Planning, Kunming, Yunnan, China
| | - Wengui Wu
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650216, Yunnan, China
| | - Shengxi Liao
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650216, Yunnan, China.
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14
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Liu Z, Dong X, Zheng G, Xu C, Wei J, Cui J, Cao X, Li H, Fang X, Wang Y, Tian H. Integrate QTL Mapping and Transcription Profiles Reveal Candidate Genes Regulating Flowering Time in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:904198. [PMID: 35837459 PMCID: PMC9274139 DOI: 10.3389/fpls.2022.904198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Flowering at the proper time is an important part of acclimation to the ambient environment and season and maximizes the plant yield. To reveal the genetic architecture and molecular regulation of flowering time in oilseed rape (Brassica napus), we performed an RNA-seq analysis of the two parents after vernalization at low temperature and combined this with quantitative trait loci (QTL) mapping in an F2 population. A genetic linkage map that included 1,017 markers merged into 268 bins and covered 793.53 cM was constructed. Two QTLs associated with flowering time were detected in the F2 population. qFTA06 was the major QTL in the 7.06 Mb interval on chromosome A06 and accounted for 19.3% of the phenotypic variation. qFTC08 was located on chromosome C06 and accounted for 8.6% of the phenotypic variation. RNA-seq analysis revealed 4,626 differentially expressed genes (DEGs) between two parents during vernalization. Integration between QTL mapping and RNA-seq analysis revealed six candidate genes involved in the regulation of flowering time through the circadian clock/photoperiod, auxin and ABA hormone signal, and cold signal transduction and vernalization pathways. These results provide insights into the molecular genetic architecture of flowering time in B. napus.
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15
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The Transcriptome and Metabolome Reveal the Potential Mechanism of Lodging Resistance in Intergeneric Hybrids between Brassica napus and Capsella bursa-pastoris. Int J Mol Sci 2022; 23:ijms23094481. [PMID: 35562871 PMCID: PMC9099622 DOI: 10.3390/ijms23094481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/06/2022] [Accepted: 04/17/2022] [Indexed: 12/04/2022] Open
Abstract
Lodging is one of the main reasons for the reduction in seed yield and is the limitation of mechanized harvesting in B. napus. The dissection of the regulatory mechanism of lodging resistance is an important goal in B. napus. In this study, the lodging resistant B. napus line, YG689, derived from the hybridization between B. napus cv. Zhongyou 821 (ZY821) and Capsella bursa-pastoris, was used to dissect the regulation mechanism of hard stem formation by integrating anatomical structure, transcriptome and metabolome analyses. It was shown that the lignocellulose content of YG689 is higher than that of ZY821, and some differentially expressed genes (DEGs) involved in the lignocellulose synthesis pathway were revealed by transcriptome analyses. Meanwhile, GC–TOF–MS and UPLC–QTOF–MS identified 40, 54, and 31 differential metabolites in the bolting stage, first flower stage, and the final flower stage. The differential accumulation of these metabolites might be associated with the lignocellulose biosynthesis in B. napus. Finally, some important genes that regulate the metabolic pathway of lignocellulose biosynthesis, such as BnaA02g18920D, BnaA10g15590D, BnaC05g48040D, and NewGene_216 were identified in B. napus through the combination of transcriptomics and metabolomics data. The present results explored the potential regulatory mechanism of lignocellulose biosynthesis, which provided a new clue for the breeding of B. napus with lodging resistance in the future.
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16
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Shao Y, Shen Y, He F, Li Z. QTL Identification for Stem Fiber, Strength and Rot Resistance in a DH Population from an Alien Introgression of Brassica napus. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030373. [PMID: 35161354 PMCID: PMC8840419 DOI: 10.3390/plants11030373] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 05/31/2023]
Abstract
Stem fiber, stem strength and stem-rot resistance are important agronomic traits in Brassica napus. To understand the molecular mechanism that controls the stem-related traits, we investigated the stem lignin (ADL), cellulose (Cel), hemicellulose (Hem) content, S/G monolignol ratio (SG), stem breaking force (BF), breaking strength (F) and Sclerotinia sclerotiorum resistance (SSR). Each trait was significantly positively or negatively correlated with more than three of the other six traits. QTL mapping for ADL, Cel, Hem, SG, BF, F and SSR were performed using a doubled haploid population derived from an intertribal B. napus introgression line 'Y689' crossed with B. napus cv. 'Westar'. A total of 67 additive QTL were identified and integrated into 55 consensus QTL by meta-analysis. Among the 55 consensus QTL, 23 (41.8%) QTL were co-located and were integrated into 11 unique QTL. The QTL by environment (Q × E) interactions were analyzed and 22 combined QTL were identified. In addition, candidate genes within the QTL intervals were proposed based on the known function of Arabidopsis orthologs. These results provided valuable information for improving lodging resistance, S. sclerotiorum resistance and mechanized harvesting of B. napus.
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Affiliation(s)
- Yujiao Shao
- College of Chemistry and Life Science, Hubei University of Education, Wuhan 430070, China;
| | - Yusen Shen
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Feifei He
- Department of Natural Sciences, Shantou Polytechnic, Shantou 515078, China;
| | - Zaiyun Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
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17
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Wang J, Hu B, Jing Y, Hu X, Guo Y, Chen J, Liu Y, Hao J, Li WX, Ning H. Detecting QTL and Candidate Genes for Plant Height in Soybean via Linkage Analysis and GWAS. FRONTIERS IN PLANT SCIENCE 2022; 12:803820. [PMID: 35126428 PMCID: PMC8813865 DOI: 10.3389/fpls.2021.803820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/20/2021] [Indexed: 05/17/2023]
Abstract
Soybean is an important global crop for edible protein and oil, and plant height is a main breeding goal which is closely related to its plant shape and yield. In this research, a high-density genetic linkage map was constructed by 1996 SNP-bin markers on the basis of a recombinant inbred line population derived from Dongnong L13 × Henong 60. A total of 33 QTL related to plant height were identified, of which five were repeatedly detected in multiple environments. In addition, a 455-germplasm population with 63,306 SNP markers was used for multi-locus association analysis. A total of 62 plant height QTN were detected, of which 26 were detected repeatedly under multiple methods. Two candidate genes, Glyma.02G133000 and Glyma.05G240600, involving in plant height were predicted by pathway analysis in the regions identified by multiple environments and backgrounds, and validated by qRT-PCR. These results enriched the soybean plant height regulatory network and contributed to molecular selection-assisted breeding.
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Affiliation(s)
- Jiajing Wang
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Bo Hu
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Yuliang Jing
- Suihua Branch of Heilongjiang Academy of Agricultural Science, Suihua, China
| | - Xiping Hu
- Key Laboratory of Crop Biotechnology Breeding of the Ministry of Agriculture, Beidahuang Kenfeng Seed Co., Ltd., Harbin, China
| | - Yue Guo
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jiankun Chen
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Yuxi Liu
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jianhui Hao
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Wen-Xia Li
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hailong Ning
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
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Transcriptomic Analysis of Sex-Associated DEGs in Female and Male Flowers of Kiwifruit (Actinidia deliciosa [A. Chev] C. F. Liang & A. R. Ferguson). HORTICULTURAE 2021. [DOI: 10.3390/horticulturae8010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Kiwifruit (Actinidia deliciosa [A. Chev.], C.V. Liang & A. R. Ferguson, 1984) is a perennial plant, with morphologically hermaphroditic and functionally dioecious flowers. Fruits of this species are berries of great commercial and nutritional importance. Nevertheless, few studies have analyzed the molecular mechanisms involved in sexual differentiation in this species. To determine these mechanisms, we performed RNA-seq in floral tissue at stage 60 on the BBCH scale in cultivar ‘Hayward’ (H, female) and a seedling from ‘Green Light’ × ‘Tomuri’ (G × T, male). From these analyses, we obtained expression profiles of 24,888 (H) and 27,027 (G × T) genes, of which 6413 showed differential transcript abundance. Genetic ontology (GO) and KEGG analysis revealed activation of pathways associated with the translation of hormonal signals, plant-pathogen interaction, metabolism of hormones, sugars, and nucleotides. The analysis of the protein-protein interaction network showed that the genes ERL1, AG, AGL8, LFY, WUS, AP2, WRKY, and CO, are crucial elements in the regulation of the hormonal response for the formation and development of anatomical reproductive structures and gametophytes. On the other hand, genes encoding four Putative S-adenosyl-L-methionine-dependent methyltransferases (Achn201401, Achn281971, Achn047771 and Achn231981) were identified, which were up-regulated mainly in the male flowers. Moreover, the expression profiles of 15 selected genes through RT-qPCR were consistent with the results of RNA-seq. Finally, this work provides gene expression-based interactions between transcription factors and effector genes from hormonal signaling pathways, development of floral organs, biological and metabolic processes or even epigenetic mechanisms which could be involved in the kiwi sex-determination. Thus, in order to decode the nature of these interactions, it could be helpful to propose new models of flower development and sex determination in the Actinidia genus.
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Helal MMU, Gill RA, Tang M, Yang L, Hu M, Yang L, Xie M, Zhao C, Cheng X, Zhang Y, Zhang X, Liu S. SNP- and Haplotype-Based GWAS of Flowering-Related Traits in Brassica napus. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112475. [PMID: 34834840 PMCID: PMC8619824 DOI: 10.3390/plants10112475] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 05/05/2023]
Abstract
Traits related to flowering time are the most promising agronomic traits that directly impact the seed yield and oil quality of rapeseed (Brassica napus L.). Developing early flowering and maturity rapeseed varieties is an important breeding objective in B. napus. Many studies have reported on days to flowering, but few have reported on budding, bolting, and the interval between bolting and DTF. Therefore, elucidating the genetic architecture of QTLs and genes regulating flowering time, we presented an integrated investigation on SNP and haplotype-based genome-wide association study of 373 diverse B. napus germplasm, which were genotyped by the 60K SNP array and were phenotyped in the four environments. The results showed that a total of 15 and 37 QTLs were detected from SNP and haplotype-based GWAS, respectively. Among them, seven QTL clusters were identified by haplotype-based GWAS. Moreover, three and eight environmentally stable QTLs were detected by SNP-GWAS and haplotype-based GWAS, respectively. By integrating the above two approaches and by co-localizing the four traits, ten (10) genomic regions were under selection on chromosomes A03, A07, A08, A10, C06, C07, and C08. Interestingly, the genomic regions FT.A07.1, FT.A08, FT.C06, and FT.C07 were identified as novel. In these ten regions, a total of 197 genes controlling FT were detected, of which 14 highly expressed DEGs were orthologous to 13 Arabidopsis thaliana genes after integration with transcriptome results. In a nutshell, the above results uncovered the genetic architecture of important agronomic traits related to flowering time and provided a basis for multiple molecular marker-trait associations in B. napus.
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Affiliation(s)
- MMU Helal
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Rafaqat Ali Gill
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Minqiang Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
- Key Laboratory of Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), College of Forestry, Hainan University, Haikou 570228, China
| | - Li Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Ming Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Lingli Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Meili Xie
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Chuanji Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Xiaohui Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Yuanyuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
- Correspondence: (Y.Z.); (X.Z.)
| | - Xiong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
- Correspondence: (Y.Z.); (X.Z.)
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
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20
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Saidi A, Hajibarat Z, Hajibarat Z. Phylogeny, gene structure and GATA genes expression in different tissues of solanaceae species. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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21
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Song J, Li B, Cui Y, Zhuo C, Gu Y, Hu K, Wen J, Yi B, Shen J, Ma C, Fu T, Tu J. QTL Mapping and Diurnal Transcriptome Analysis Identify Candidate Genes Regulating Brassica napus Flowering Time. Int J Mol Sci 2021; 22:ijms22147559. [PMID: 34299178 PMCID: PMC8305928 DOI: 10.3390/ijms22147559] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/04/2021] [Accepted: 07/07/2021] [Indexed: 12/16/2022] Open
Abstract
Timely flowering is important for seed formation and maximization of rapeseed (Brassica napus) yield. Here, we performed flowering-time quantitative trait loci (QTL) mapping using a double haploid (DH) population grown in three environments to study the genetic architecture. Brassica 60 K Illumina Infinium™ single nucleotide polymorphism (SNP) array and simple sequence repeat (SSR) markers were used for genotyping of the DH population, and a high-density genetic linkage map was constructed. QTL analysis of flowering time from the three environments revealed five consensus QTLs, including two major QTLs. A major QTL located on chromosome A03 was detected specifically in the semi-winter rapeseed growing region, and the one on chromosome C08 was detected in all environments. Ribonucleic acid sequencing (RNA-seq) was performed on the parents’ leaves at seven time-points in a day to determine differentially expressed genes (DEGs). The biological processes and pathways with significant enrichment of DEGs were obtained. The DEGs in the QTL intervals were analyzed, and four flowering time-related candidate genes were found. These results lay a foundation for the genetic regulation of rapeseed flowering time and create a rapeseed gene expression library for seven time-points in a day.
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Affiliation(s)
- Jurong Song
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Bao Li
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Yanke Cui
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Chenjian Zhuo
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Yuanguo Gu
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
- Correspondence:
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22
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Rahman H, Kebede B. Mapping of seed quality traits in the C genome of Brassica napus by using a population carrying genome content of B. oleracea and their effect on other traits. THE PLANT GENOME 2021; 14:e20078. [PMID: 33818008 DOI: 10.1002/tpg2.20078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 11/21/2020] [Indexed: 06/12/2023]
Abstract
Increasing seed oil and protein contents and reducing the content of seed glucosinolates (GSLs) in Brassica oilseed crops are important objectives in breeding. By using an oilseed rape (B. napus L.) doubled-haploid (DH) population carrying genome content introgressed from Chinese kale (B. oleracea L.), we mapped quantitative trait loci (QTL) for these seed quality traits and investigated their effect on other traits including seed yield. A stable QTL for seed oil content was identified on chromosome C5 at 40-42 Mb position and a QTL for seed GSL content was identified on C9 at 7-8 Mb position. The C5 and C9 QTL alleles for high oil and GSL contents were derived from Chinese kale, demonstrating that high-oil QTL allele can be found in the parental species of oilseed rape. The low-GSL QTL allele of C9 exerted a significant positive effect on seed protein content, demonstrating that selection for this QTL allele contributed to higher protein content in canola seed. These two QTL were not affected by field environmental conditions and did not exert a significant effect on days to flowering and seed yield. Thus, the genomic regions and the molecular markers identified in this study should be useful in molecular breeding of the seed quality traits in oilseed rape.
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Affiliation(s)
- Habibur Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Berisso Kebede
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
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23
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Han X, Xu ZR, Zhou L, Han CY, Zhang YM. Identification of QTNs and their candidate genes for flowering time and plant height in soybean using multi-locus genome-wide association studies. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:39. [PMID: 37309439 PMCID: PMC10236079 DOI: 10.1007/s11032-021-01230-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/06/2021] [Indexed: 06/14/2023]
Abstract
Flowering time (FT) and plant height (PH) are important agronomic traits in soybean. However, their genetic foundations are not fully understood. Thus, in this study, a total of 106,013 single nucleotide polymorphisms in 286 soybean accessions were used to associate with the first and full FT (FT1 and FT2) and PH in 4 environments and their BLUP values using 6 multi-locus genome-wide association study methods. As a result, 38, 43, and 27 stable quantitative trait nucleotides (QTNs) were identified, respectively, for FT1, FT2, and PH across at least 3 methods and/or environments. Among these QTNs for FT1, FT2, and PH, 31, 36, and 21 were found to have significant phenotype differences across 2 alleles; 22, 18, and 13 were consistent with the corresponding loci in previous studies; 13 and 8 genes, with more than average expression level, around 64 FT and 27 PH QTNs were predicted as their corresponding candidate genes. Among these candidate genes, GmPRR3b, and GmGIa for FT, and GmTFL1b for PH were known, while some were new, e.g., GmPHYA4, GmVRN5, GmFPA, and GmSPA1 for FT, and Glyma.02g300200, GmFPA, and Glyma.13g339800 for PH. All the validated QTNs were used to design the best cross-combinations in 2 FT directions. In each FT direction, the best 5 cross-combinations were predicted, such as Heihe 54 × Qincha 1 for early FT, and Yingdejiadou × Wuhuabayuehuang for late FT. This study provides solid foundations for genetic basis, molecular biology, and breeding by design of soybean FT and PH. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01230-3.
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Affiliation(s)
- Xu Han
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zhuo-Ran Xu
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Ling Zhou
- Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Chun-Yu Han
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
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Sun X, Gao Y, Lu Y, Zhang X, Luo S, Li X, Liu M, Feng D, Gu A, Chen X, Xuan S, Wang Y, Shen S, Bonnema G, Zhao J. Genetic analysis of the "head top shape" quality trait of Chinese cabbage and its association with rosette leaf variation. HORTICULTURE RESEARCH 2021; 8:106. [PMID: 33931629 PMCID: PMC8087666 DOI: 10.1038/s41438-021-00541-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/10/2021] [Accepted: 03/05/2021] [Indexed: 05/08/2023]
Abstract
The agricultural and consumer quality of Chinese cabbage is determined by its shape. The shape is defined by the folding of the heading leaves, which defines the head top shape (HTS). The overlapping HTS, in which the heading leaves curve inward and overlap at the top, is the shape preferred by consumers. To understand the genetic regulation of HTS, we generated a large segregating F2 population from a cross between pak choi and Chinese cabbage, with phenotypes ranging from nonheading to heading with either outward curving or inward curving overlapping heading leaves. HTS was correlated with plant height, outer/rosette leaf length, and petiole length. A high-density genetic map was constructed. Quantitative trait locus (QTL) analysis resulted in the identification of 22 QTLs for leafy head-related traits, which included five HTS QTLs. Bulked segregant analysis (BSA) was used to confirm HTS QTLs and identify candidate genes based on informative single-nucleotide polymorphisms. Interestingly, the HTS QTLs colocalized with QTLs for plant height, outer/rosette leaf, and petiole length, consistent with the observed phenotypic correlations. Combined QTL analysis and BSA laid a foundation for molecular marker-assisted breeding of Chinese cabbage HTS and directions for further research on the genetic regulation of this trait.
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Affiliation(s)
- Xiaoxue Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Ying Gao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Yin Lu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Xiaomeng Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Shuangxia Luo
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Xing Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Mengyang Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Daling Feng
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Aixia Gu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Xueping Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Shuxin Xuan
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Yanhua Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Shuxing Shen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
| | - Guusje Bonnema
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
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Sun CY, Yang YM, Jia L, Liu XQ, Xu HQ, Lv HY, Huang ZW, Zhang D. QTL mapping of the genetic basis of stem diameter in soybean. PLANTA 2021; 253:109. [PMID: 33871705 DOI: 10.1007/s00425-021-03628-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
MAIN CONCLUSION QTL mapping of stem diameter was carried out in three RIL populations using a high-density genetic map, and candidate genes related to stem diameter were predicted. Stem diameter is an important agronomic trait affecting soybean lodging and productivity. However, this trait is underexploited, and the underlying genetic mechanism in soybean remains unclear. In this study, three recombinant inbred line (RIL) populations, including 156 F10 lines from Nannong 94-156 × Bogao (N × B), 127 F9 lines from Dongnong 50 × Williams 82 (D × W), and 146 F9 lines from Suinong 14 × Enrei (S × E), were used to identify QTLs for soybean stem diameter across multiple environments. Phenotype analysis revealed that stem diameter exhibited strong positive correlations with plant height and 100-seed weight, two of the most important yield components. A total of 12 QTLs for stem diameter were identified on eight chromosomes across three RIL populations and five environments. The most influential QTL that was stably identified across all the populations and environments, q11, explained 12.58-26.63% of the phenotypic variation. Detection of several environment-specific QTLs, including q14, q16, and q20, suggests that environments may also have important effects in shaping the natural variation in soybean stem diameter. Furthermore, we predicted candidate genes underlying the QTLs and found that several promising candidate genes may be responsible for the variation in stem diameter in soybean. Overall, the markers/genes linked closely or underlying the major QTLs may be used for marker-assisted selection of soybean varieties to enhance lodging resistance and even yield. Our results lay the foundation for the fine mapping of stem development-related genes to reveal the molecular mechanisms.
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Affiliation(s)
- Chong-Yuan Sun
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yu-Ming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lin Jia
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiao-Qian Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huan-Qing Xu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hai-Yan Lv
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhong-Wen Huang
- School of Life Science and Technology, Henan Institute of Science and Technology/Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, 453003, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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26
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Scheben A, Severn-Ellis AA, Patel D, Pradhan A, Rae SJ, Batley J, Edwards D. Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus. BMC PLANT BIOLOGY 2020; 20:546. [PMID: 33287721 PMCID: PMC7720618 DOI: 10.1186/s12870-020-02756-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/25/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Brassica napus is an important oilseed crop cultivated worldwide. During domestication and breeding of B. napus, flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering in B. napus. An F2 mapping population was derived from a cross between an early-flowering spring type and a late-flowering winter type. RESULTS Flowering time in the mapping population differed by up to 25 days between individuals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ~ 12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3981.31 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trait locus (QTL) on chromosome C2 was detected, covering eight flowering time genes including FLC. CONCLUSIONS These findings demonstrate the effectiveness of the ddRAD approach to sample the B. napus genome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F2 populations. Quality filtering and genotype correction and imputation can substantially reduce these error rates and allow effective linkage mapping and QTL analysis.
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Affiliation(s)
- Armin Scheben
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Anita A Severn-Ellis
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Dhwani Patel
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Aneeta Pradhan
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Stephen J Rae
- BASF Agricultural Solutions Belgium NV, BASF Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052, Ghent, Belgium
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.
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Zhu W, Guo Y, Chen Y, Wu D, Jiang L. Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus. BMC PLANT BIOLOGY 2020; 20:543. [PMID: 33276730 PMCID: PMC7716463 DOI: 10.1186/s12870-020-02752-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/24/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Transcription factors GATAs are involved in plant developmental processes and respond to environmental stresses through binding DNA regulatory regions to regulate their downstream genes. However, little information on the GATA genes in Brassica napus is available. The release of the reference genome of B. napus provides a good opportunity to perform a genome-wide characterization of GATA family genes in rapeseed. RESULTS In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus, which were classified into four subfamilies based on phylogenetic analysis and their domain structures. The amino acids of BnGATAs were obvious divergence among four subfamilies in terms of their GATA domains, structures and motif compositions. Gene duplication and synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distributions of BnGATAs in a core collection germplasm are probably associated with functional disparity under environmental stress condition in different genotypes of B. napus. CONCLUSION The present study was investigated genomic structures, evolution features, expression patterns and SNP distributions of 96 BnGATAs. The results enrich our understanding of the GATA genes in rapeseed.
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Affiliation(s)
- Weizhuo Zhu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Yiyi Guo
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Yeke Chen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Dezhi Wu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China.
| | - Lixi Jiang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
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Wang X, Zheng M, Liu H, Zhang L, Chen F, Zhang W, Fan S, Peng M, Hu M, Wang H, Zhang J, Hua W. Fine-mapping and transcriptome analysis of a candidate gene controlling plant height in Brassica napus L. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:42. [PMID: 32175009 PMCID: PMC7063735 DOI: 10.1186/s13068-020-01687-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 02/22/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Brassica napus provides approximately 13-16% of global vegetable oil for human consumption and biodiesel production. Plant height (PH) is a key trait that affects plant architecture, seed yield and harvest index. However, the genetic mechanism of PH in B. napus is poorly understood. RESULTS A dwarf mutant df59 was isolated from a large-scale screening of an ethyl methanesulphonate-mutagenized rapeseed variety Ningyou 18. A genetic analysis showed that the dwarfism phenotype was controlled by one semi-dominant gene, which was mapped on C9 chromosome by quantitative trait loci sequencing analysis and designated as BnaDwf.C9. To fine-map BnaDwf.C9, two F2 populations were constructed from crosses between conventional rapeseed cultivars (Zhongshuang 11 and Holly) and df59. BnaDwf.C9 was fine-mapped to the region between single-nucleotide polymorphism (SNP) markers M14 and M4, corresponding to a 120.87-kb interval of the B. napus 'Darmor-bzh' genome. Within this interval, seven, eight and nine annotated or predicted genes were identified in "Darmor-bzh", "Ningyou 7" and "Zhongshuang 11" reference genomes, respectively. In addition, a comparative transcriptome analysis was performed using stem tips from Ningyou 18 and df59 at the stem elongation stage. In total, 3995 differentially expressed genes (DEGs) were identified. Among them, 118 DEGs were clustered in plant hormone-related signal transduction pathways, including 81 DEGs were enriched in auxin signal transduction. Combining the results of fine-mapping and transcriptome analyses, BnaC09g20450D was considered a candidate gene for BnaDwf.C9, which contains a SNP that co-segregated in 4746 individuals. Finally, a PCR-based marker was developed based on the SNP in BnaC09g20450D. CONCLUSIONS The combination of quantitative trait loci sequencing, fine-mapping and genome-wide transcriptomic analysis revealed one candidate gene located within the confidence interval of 120.87-kb region. This study provides a new genetic resource for semi-dwarf breeding and new insights into understanding the genetic architecture of PH in B. napus.
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Affiliation(s)
- Xiaodong 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 and Rural Affairs, Wuhan, China
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Ming Zheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Hongfang 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 and Rural Affairs, Wuhan, China
| | - Liang Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Feng Chen
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Wei Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Shihang Fan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Menlu Peng
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Maolong Hu
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, 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 and Rural Affairs, Wuhan, China
| | - Jiefu Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
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Zhang R, Jia Z, Ma X, Ma H, Zhao Y. Characterising the morphological characters and carbohydrate metabolism of oat culms and their association with lodging resistance. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:267-276. [PMID: 31631474 DOI: 10.1111/plb.13058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 10/12/2019] [Indexed: 06/10/2023]
Abstract
Lodging resistance can be improved by enhancing the mechanical strength of culms, and culm carbohydrates could improve this mechanical strength. Culm carbohydrates can regulate development of the culm and affect its toughness. The present study determines the relationship between lodging and carbohydrate content in oat culms. Field experiments were conducted in alpine regions in 2017 and 2018 using three oat varieties with different lodging resistance. Lodging-related morphological characteristics were directly determined and culm carbohydrate content and enzyme activity related to cellulose synthesis and sucrose metabolism were evaluated with ultraviolet spectrophotometry. Results showed that the lower the gravity height or the lower ratio of gravity height to plant height, the stronger the lodging resistance of the varieties. Higher culm nonstructural (NSC) and structural (SC) carbohydrate content contributed to the ability of culms to resist lodging, especially the content of cellulose and sucrose. PCA showed that sucrose metabolism and SC content were closely related to lodging resistance. Correlation analysis showed that the lodging index (LI) was significantly negatively correlated with NSC. Sucrose content was highly and significantly positively correlated with NSC. Additionally, the activities of sucrose phosphate synthase (SPS) and sucrose synthase (SS) were highly and significantly positively correlated with sucrose and cellulose content. The relationship between field characters and oat lodging, as well as the regulatory mechanism of carbohydrate content on lodging resistance of the culm are discussed.
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Affiliation(s)
- R Zhang
- Key Laboratory of Grassland Ecosystem, College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Z Jia
- Academy of Animal Sciences and Veterinary, Qinghai University, Xining, China
| | - X Ma
- Academy of Animal Sciences and Veterinary, Qinghai University, Xining, China
| | - H Ma
- Key Laboratory of Grassland Ecosystem, College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Y Zhao
- Key Laboratory of Grassland Ecosystem, College of Grassland Science, Gansu Agricultural University, Lanzhou, China
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30
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Xu Y, Zhang B, Ma N, Liu X, Qin M, Zhang Y, Wang K, Guo N, Zuo K, Liu X, Zhang M, Huang Z, Xu A. Quantitative Trait Locus Mapping and Identification of Candidate Genes Controlling Flowering Time in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2020; 11:626205. [PMID: 33613591 PMCID: PMC7886670 DOI: 10.3389/fpls.2020.626205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/30/2020] [Indexed: 05/02/2023]
Abstract
Flowering time plays a vital role in determining the life-cycle period, yield, and seed quality of rapeseed (Brassica napus L.) in certain environments. Quantitative trait locus (QTL) mapping to identify the genetic architecture of genes controlling flowering time helps accelerate the early maturity breeding process. In this study, simple sequence repeats (SSR) and specific-locus amplified fragment sequencing (SLAF-seq) technologies were adopted to map the QTLs for flowering time in four environments. As a result, three target intervals, FTA09, FTA10, and FTC05 were identified. Among this, FTA09 was considered as a novel interval, FTA10 and FTC05 as stable regions. Based on the parental re-sequencing data, 7,022 single nucleotide polymorphisms (SNPs) and 2,195 insertion-deletions (InDels) between the two parents were identified in these three target regions. A total of 186 genes possessed genetic variations in these intervals, 14 of which were related to flowering time involved in photoperiod, circadian clock, vernalization, and gibberellin pathways. Six InDel markers linked to flowering time were developed in the three target intervals, indicating that the results were credible in this study. These results laid a good foundation for further genetic studies on flowering-time regulation in B. napus L.
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Affiliation(s)
- Yu Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Bingbing Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Ning Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Xia Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
- Market Supervision Administration, Yanchi, China
| | - Mengfan Qin
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Yan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Kai Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Na Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Kaifeng Zuo
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Xiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Miao Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
| | - Zhen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
- Zhen Huang,
| | - Aixia Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, China
- *Correspondence: Aixia Xu,
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Stansell Z, Farnham M, Björkman T. Complex Horticultural Quality Traits in Broccoli Are Illuminated by Evaluation of the Immortal BolTBDH Mapping Population. FRONTIERS IN PLANT SCIENCE 2019; 10:1104. [PMID: 31620146 PMCID: PMC6759917 DOI: 10.3389/fpls.2019.01104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/12/2019] [Indexed: 05/19/2023]
Abstract
Improving horticultural quality in regionally adapted broccoli (Brassica oleracea var. italica) and other B. oleracea crops is challenging due to complex genetic control of traits affecting morphology, development, and yield. Mapping horticultural quality traits to genomic loci is an essential step in these improvement efforts. Understanding the mechanisms underlying horticultural quality enables multi-trait marker-assisted selection for improved, resilient, and regionally adapted B. oleracea germplasm. The publicly-available biparental double-haploid BolTBDH mapping population (Chinese kale × broccoli; N = 175) was evaluated for 25 horticultural traits in six trait classes (architecture, biomass, phenology, leaf morphology, floral morphology, and head quality) by multiple quantitative trait loci mapping using 1,881 genotype-by-sequencing derived single nucleotide polymorphisms. The physical locations of 56 single and 41 epistatic quantitative trait locus (QTL) were identified. Four head quality QTL (OQ_C03@57.0, OQ_C04@33.3, OQ_CC08@25.5, and OQ_C09@49.7) explain a cumulative 81.9% of phenotypic variance in the broccoli heading phenotype, contain the FLOWERING LOCUS C (FLC) homologs Bo9g173400 and Bo9g173370, and exhibit epistatic effects. Three key genomic hotspots associated with pleiotropic control of the broccoli heading phenotype were identified. One phenology hotspot reduces days to flowering by 7.0 days and includes an additional FLC homolog Bo3g024250 that does not exhibit epistatic effects with the three horticultural quality hotspots. Strong candidates for other horticultural traits were identified: BoLMI1 (Bo3g002560) associated with serrated leaf margins and leaf apex shape, BoCCD4 (Bo3g158650) implicated in flower color, and BoAP2 (Bo1g004960) implicated in the hooked sepal horticultural trait. The BolTBDH population provides a framework for B. oleracea improvement by targeting key genomic loci contributing to high horticultural quality broccoli and enabling de novo mapping of currently unexplored traits.
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Affiliation(s)
- Zachary Stansell
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- Cornell Agritech, Cornell University, Geneva, NY, United States
- *Correspondence: Zachary Stansell,
| | - Mark Farnham
- USDA-ARS Vegetable Laboratory, Department of Horticulture, Charleston, SC, United States
| | - Thomas Björkman
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- Cornell Agritech, Cornell University, Geneva, NY, United States
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Salentijn EMJ, Petit J, Trindade LM. The Complex Interactions Between Flowering Behavior and Fiber Quality in Hemp. FRONTIERS IN PLANT SCIENCE 2019; 10:614. [PMID: 31156677 PMCID: PMC6532435 DOI: 10.3389/fpls.2019.00614] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/25/2019] [Indexed: 05/05/2023]
Abstract
Hemp, Cannabis sativa L., is a sustainable multipurpose fiber crop with high nutrient and water use efficiency and with biomass of excellent quality for textile fibers and construction materials. The yield and quality of hemp biomass are largely determined by the genetic background of the hemp cultivar but are also strongly affected by environmental factors, such as temperature and photoperiod. Hemp is a facultative short-day plant, characterized by a strong adaptation to photoperiod and a great influence of environmental factors on important agronomic traits such as "flowering-time" and "sex determination." This sensitivity of hemp can cause a considerable degree of heterogeneity, leading to unforeseen yield reductions. Fiber quality for instance is influenced by the developmental stage of hemp at harvest. Also, male and female plants differ in stature and produce fibers with different properties and quality. Next to these causes, there is evidence for specific genotypic variation in fiber quality among hemp accessions. Before improved hemp cultivars can be developed, with specific flowering-times and fiber qualities, and adapted to different geographical regions, a better understanding of the molecular mechanisms controlling important phenological traits such as "flowering-time" and "sex determination" in relation to fiber quality in hemp is required. It is well known that genetic factors play a major role in the outcome of both phenological traits, but the major molecular factors involved in this mechanism are not characterized in hemp. Genome sequences and transcriptome data are available but their analysis mainly focused on the cannabinoid pathway for medical purposes. Herein, we review the current knowledge of phenotypic and genetic data available for "flowering-time," "sex determination," and "fiber quality" in short-day and dioecious crops, respectively, and compare them with the situation in hemp. A picture emerges for several controlling key genes, for which natural genetic variation may lead to desired flowering behavior, including examples of pleiotropic effects on yield quality and on carbon partitioning. Finally, we discuss the prospects for using this knowledge for the molecular breeding of this sustainable crop via a candidate gene approach.
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Shah S, Karunarathna NL, Jung C, Emrani N. An APETALA1 ortholog affects plant architecture and seed yield component in oilseed rape (Brassica napus L.). BMC PLANT BIOLOGY 2018; 18:380. [PMID: 30594150 PMCID: PMC6310979 DOI: 10.1186/s12870-018-1606-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 12/17/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Increasing the productivity of rapeseed as one of the widely cultivated oil crops in the world is of upmost importance. As flowering time and plant architecture play a key role in the regulation of rapeseed yield, understanding the genetic mechanism underlying these traits can boost the rapeseed breeding. Meristem identity genes are known to have pleiotropic effects on plant architecture and seed yield in various crops. To understand the function of one of the meristem identity genes, APETALA1 (AP1) in rapeseed, we performed phenotypic analysis of TILLING mutants under greenhouse conditions. Three stop codon mutant families carrying a mutation in Bna.AP1.A02 paralog were analyzed for different plant architecture and seed yield-related traits. RESULTS It was evident that stop codon mutation in the K domain of Bna.AP1.A02 paralog caused significant changes in flower morphology as well as plant architecture related traits like plant height, branch height, and branch number. Furthermore, yield-related traits like seed yield per plant and number of seeds per plants were also significantly altered in the same mutant family. Apart from phenotypic changes, stop codon mutation in K domain of Bna.AP1.A02 paralog also altered the expression of putative downstream target genes like Bna.TFL1 and Bna.FUL in shoot apical meristem (SAM) of rapeseed. Mutant plants carrying stop codon mutations in the COOH domain of Bna.AP1.A02 paralog did not have a significant effect on plant architecture, yield-related traits or the expression of the downstream targets. CONCLUSIONS We found that Bna.AP1.A02 paralog has pleiotropic effect on plant architecture and yield-related traits in rapeseed. The allele we found in the current study with a beneficial effect on seed yield can be incorporated into rapeseed breeding pool to develop new varieties.
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Affiliation(s)
- Smit Shah
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098 Kiel, Germany
| | - Nirosha L. Karunarathna
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098 Kiel, Germany
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098 Kiel, Germany
| | - Nazgol Emrani
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098 Kiel, Germany
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Leijten W, Koes R, Roobeek I, Frugis G. Translating Flowering Time From Arabidopsis thaliana to Brassicaceae and Asteraceae Crop Species. PLANTS 2018; 7:plants7040111. [PMID: 30558374 PMCID: PMC6313873 DOI: 10.3390/plants7040111] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/07/2018] [Accepted: 12/13/2018] [Indexed: 12/31/2022]
Abstract
Flowering and seed set are essential for plant species to survive, hence plants need to adapt to highly variable environments to flower in the most favorable conditions. Endogenous cues such as plant age and hormones coordinate with the environmental cues like temperature and day length to determine optimal time for the transition from vegetative to reproductive growth. In a breeding context, controlling flowering time would help to speed up the production of new hybrids and produce high yield throughout the year. The flowering time genetic network is extensively studied in the plant model species Arabidopsis thaliana, however this knowledge is still limited in most crops. This article reviews evidence of conservation and divergence of flowering time regulation in A. thaliana with its related crop species in the Brassicaceae and with more distant vegetable crops within the Asteraceae family. Despite the overall conservation of most flowering time pathways in these families, many genes controlling this trait remain elusive, and the function of most Arabidopsis homologs in these crops are yet to be determined. However, the knowledge gathered so far in both model and crop species can be already exploited in vegetable crop breeding for flowering time control.
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Affiliation(s)
- Willeke Leijten
- ENZA Zaden Research & Development B.V., Haling 1E, 1602 DB Enkhuizen, The Netherlands.
| | - Ronald Koes
- Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Ilja Roobeek
- ENZA Zaden Research & Development B.V., Haling 1E, 1602 DB Enkhuizen, The Netherlands.
| | - Giovanna Frugis
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Operative Unit of Rome, Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km. 29,300 ⁻ 00015, Monterotondo Scalo, Roma, Italy.
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Huai Z, Peng L, Wang S, Zhao H, Shi L, Xu F. Identification and Characterization of an Arabidopsis thaliana Mutant lbt With High Tolerance to Boron Deficiency. FRONTIERS IN PLANT SCIENCE 2018; 9:736. [PMID: 29915610 PMCID: PMC5994474 DOI: 10.3389/fpls.2018.00736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/15/2018] [Indexed: 06/01/2023]
Abstract
Boron (B) is an essential micronutrient of plants. In the present study, we characterized an Arabidopsis mutant lbt with significant low-boron tolerance that was identified based on our previous mapping of QTL for B efficiency in Arabidopsis. Multiple nutrient-deficiency analyses point out that lbt mutant is insensitive to only B-limitation stress. Compared with wild-type Col-0, the fresh weight, leaf area, root length and root elongation rate of lbt mutant were significantly improved under B deficiency during vegetative growth. lbt mutant also showed the improvements in plant height, branches and inflorescences compared with Col-0 during the reproductive stage under B limitation. Ultrastructure analysis of the leaves showed that starch accumulation in lbt mutant was significantly diminished compared with Col-0. Furthermore, there were no significant differences in the expression of transporter-related genes and B concentrations between Col-0 and lbt mutant under both normal B and low-B conditions. These results suggest that lbt mutant has a lower B demand than Col-0. Genetic analysis suggests that the low-B tolerant phenotype of lbt mutant is under the control of a monogenic recessive gene. Based on the high-density SNP linkage genetic map, only one QTL for low-B tolerance was mapped on chromosome 4 between 10.4 and 14.8 Mb. No any reported B-relative genes exist in the QTL interval, suggesting that a gene with unknown function controls the tolerance of lbt to B limitation. Taken together, lbt is a low-B tolerant mutant that does not depend on the uptake or transport of B and is controlled by a monogenic recessive gene mapped on chromosome 4, and cloning and functional analysis of LBT gene are expected to reveal novel mechanisms for plant resistance to B deficiency.
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Affiliation(s)
- Zexun Huai
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Center, Huazhong Agricultural University, Wuhan, China
| | - Lishun Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Center, Huazhong Agricultural University, Wuhan, China
| | - Hua Zhao
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Center, Huazhong Agricultural University, Wuhan, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Center, Huazhong Agricultural University, Wuhan, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Center, Huazhong Agricultural University, Wuhan, China
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