1
|
Fang Y, Zhang X, Liu H, Wu J, Qi F, Sun Z, Zheng Z, Dong W, Huang B. Identification of quantitative trait loci and development of diagnostic markers for growth habit traits in peanut (Arachis hypogaea L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:105. [PMID: 37027030 PMCID: PMC10082100 DOI: 10.1007/s00122-023-04327-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 02/20/2023] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE QTLs for growth habit are identified on Arahy.15 and Arahy.06 in peanut, and diagnostic markers are developed and validated for further use in marker-assisted breeding. Peanut is a unique legume crop because its pods develop and mature underground. The pegs derive from flowers following pollination, then reach the ground and develop into pods in the soil. Pod number per plant is influenced by peanut growth habit (GH) that has been categorized into four types, including erect, bunch, spreading and prostrate. Restricting pod development at the plant base, as would be the case for peanut plants with upright lateral branches, would decrease pod yield. On the other hand, GH characterized by spreading lateral branches on the ground would facilitate pod formation on the nodes, thereby increasing yield potential. We describe herein an investigation into the GH traits of 521 peanut recombinant inbred lines grown in three distinct environments. Quantitative trait loci (QTLs) for GH were identified on linkage group (LG) 15 between 203.1 and 204.2 cM and on LG 16 from 139.1 to 139.3 cM. Analysis of resequencing data in the identified QTL regions revealed that single nucleotide polymorphism (SNP) or insertion and/or deletion (INDEL) at Arahy15.156854742, Arahy15.156931574, Arahy15.156976352 and Arahy06.111973258 may affect the functions of their respective candidate genes, Arahy.QV02Z8, Arahy.509QUQ, Arahy.ATH5WE and Arahy.SC7TJM. These SNPs and INDELs in relation to peanut GH were further developed for KASP genotyping and tested on a panel of 77 peanut accessions with distinct GH features. This study validates four diagnostic markers that may be used to distinguish erect/bunch peanuts from spreading/prostrate peanuts, thereby facilitating marker-assisted selection for GH traits in peanut breeding.
Collapse
Affiliation(s)
- Yuanjin Fang
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Henan Academy of Agricultural Sciences, Henan Institute of Crop Molecular Breeding, Shennong Laboratory, Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Xinyou Zhang
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
- Henan Academy of Agricultural Sciences, Henan Institute of Crop Molecular Breeding, Shennong Laboratory, Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China.
| | - Hua Liu
- Henan Academy of Agricultural Sciences, Henan Institute of Crop Molecular Breeding, Shennong Laboratory, Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Jihua Wu
- Shangqiu Academy of Agriculture and Forestry, Shangqiu, 476002, China
| | - Feiyan Qi
- Henan Academy of Agricultural Sciences, Henan Institute of Crop Molecular Breeding, Shennong Laboratory, Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Ziqi Sun
- Henan Academy of Agricultural Sciences, Henan Institute of Crop Molecular Breeding, Shennong Laboratory, Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Zheng Zheng
- Henan Academy of Agricultural Sciences, Henan Institute of Crop Molecular Breeding, Shennong Laboratory, Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Wenzhao Dong
- Henan Academy of Agricultural Sciences, Henan Institute of Crop Molecular Breeding, Shennong Laboratory, Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Bingyan Huang
- Henan Academy of Agricultural Sciences, Henan Institute of Crop Molecular Breeding, Shennong Laboratory, Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China.
| |
Collapse
|
2
|
Qi Y, Wang L, Li W, Xie Y, Zhao W, Dang Z, Li W, Zhao L, Zhang J. Phenotypic analysis of Longya-10 × pale flax hybrid progeny and identification of candidate genes regulating prostrate/erect growth in flax plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1044415. [PMID: 36561460 PMCID: PMC9763623 DOI: 10.3389/fpls.2022.1044415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Flax is a dual-purpose crop that is important for oil and fiber production. The growth habit is one of the crucial targets of selection during flax domestication. Wild hybridization between cultivated flax and wild flax can produce superior germplasms for flax breeding and facilitate the study of the genetic mechanism underlying agronomically important traits. In this study, we used pale flax, Linum grandiflorum, and L. perenne to pollinate Longya-10. Only pale flax interspecific hybrids were obtained, and the trait analysis of the F1 and F2 generations showed that the traits analyzed in this study exhibited disparate genetic characteristics. In the F1 generation, only one trait, i.e., the number of capsules per plant (140) showed significant heterosis, while the characteristics of other traits were closely associated with those of the parents or a decline in hybrid phenotypes. The traits of the F2 generation were widely separated, and the variation coefficient ranged from 9.96% to 146.15%. The quantitative trait locus underlying growth habit was preliminarily found to be situated on chromosome 2 through Bulked-segregant analysis sequencing. Then linkage mapping analysis was performed to fine-map GH2.1 to a 23.5-kb interval containing 4 genes. Among them, L.us.o.m.scaffold22.109 and L.us.o.m.scaffold22.112 contained nonsynonymous SNPs with Δindex=1. Combined with the qRT-PCR results, the two genes might be possible candidate genes for GH2.1. This study will contribute to the development of important germplasms for flax breeding, which would facilitate the elucidation of the genetic mechanisms regulating the growth habit and development of an ideal architecture for the flax plant.
Collapse
|
3
|
Pan J, Zhou X, Ahmad N, Zhang K, Tang R, Zhao H, Jiang J, Tian M, Li C, Li A, Zhang X, He L, Ma J, Li X, Tian R, Ma C, Pandey MK, Varshney RK, Wang X, Zhao C. BSA‑seq and genetic mapping identified candidate genes for branching habit in peanut. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4457-4468. [PMID: 36181525 DOI: 10.1007/s00122-022-04231-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
The candidate gene AhLBA1 controlling lateral branch angel of peanut was fine-mapped to a 136.65-kb physical region on chromosome 15 using the BSA-seq and QTL mapping. Lateral branch angel (LBA) is an important plant architecture trait of peanut, which plays key role in lodging, peg soil penetration and pod yield. However, there are few reports of fine mapping and quantitative trait loci (QTLs)/cloned genes for LBA in peanut. In this project, a mapping population was constructed using a spreading variety Tifrunner and the erect variety Fuhuasheng. Through bulked segregant analysis sequencing (BSA-seq), a major gene related to LBA, named as AhLBA1, was preliminarily mapped at the region of Chr.15: 150-160 Mb. Then, using traditional QTL approach, AhLBA1 was narrowed to a 1.12 cM region, corresponding to a 136.65-kb physical interval of the reference genome. Of the nine genes housed in this region, three of them were involved in hormone metabolism and regulation, including one "F-box protein" and two "2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase (2OG oxygenase)" encoding genes. In addition, we found that the level of some classes of cytokinin (CK), auxin and ethylene showed significant differences between spreading and erect peanuts at the junction of main stem and lateral branch. These findings will aid further elucidation of the genetic mechanism of LBA in peanut and facilitating marker-assisted selection (MAS) in the future breeding program.
Collapse
Affiliation(s)
- Jiaowen Pan
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Ximeng Zhou
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Naveed Ahmad
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Kun Zhang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Agricultural Science and Technology, Shandong Agriculture and Engineering University, Jinan, 250100, People's Republic of China
| | - Ronghua Tang
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Huiling Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Jing Jiang
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Mengdi Tian
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, People's Republic of China
| | - Changsheng Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Aiqin Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Xianying Zhang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Liangqiong He
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Jing Ma
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Xiaojie Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Ruizheng Tian
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China.
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China.
| |
Collapse
|
4
|
A Genomic BSAseq Approach for the Characterization of QTLs Underlying Resistance to Fusarium oxysporum in Eggplant. Cells 2022; 11:cells11162548. [PMID: 36010625 PMCID: PMC9406753 DOI: 10.3390/cells11162548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Eggplant (Solanum melongena L.), similar to many other crops, suffers from soil-borne diseases, including Fusarium oxysporum f. sp. melongenae (Fom), causing wilting and heavy yield loss. To date, the genetic factors underlying plant responses to Fom are not well known. We previously developed a Recombinant Inbred Lines (RILs) population using as a female parent the fully resistant line ‘305E40’ and as a male parent the partially resistant line ‘67/3’. The fully resistant trait to Fom was introgressed from the allied species S. aethiopicum. In this work, the RIL population was assessed for the responses to Fom and by using a genomic mapping approach, two major QTLs on chromosomes CH02 and CH11 were identified, associated with the full and partial resistance trait to Fom, respectively. A targeted BSAseq procedure in which Illumina reads bulks of RILs grouped according to their resistance score was aligned to the appropriate reference genomes highlighted differentially enriched regions between resistant/susceptible progeny in the genomic regions underlying both QTLs. The characterization of such regions allowed us to identify the most reliable candidate genes for the two resistance traits. With the aim of revealing exclusive species-specific contigs and scaffolds inherited from the allied species and thus associated with the full resistance trait, a draft de-novo assembly of available Illumina sequences of the ‘305E40’ parent was developed to better resolve the non-recombining genomic region on its CH02 carrying the introgressed Fom resistance locus from S. aethiopicum.
Collapse
|
5
|
Song H, Guo Z, Zhang X, Sui J. De novo genes in Arachis hypogaea cv. Tifrunner: systematic identification, molecular evolution, and potential contributions to cultivated peanut. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1081-1095. [PMID: 35748398 DOI: 10.1111/tpj.15875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
De novo genes are derived from non-coding sequences, and they can play essential roles in organisms. Cultivated peanut (Arachis hypogaea) is a major oil and protein crop derived from a cross between Arachis duranensis and Arachis ipaensis. However, few de novo genes have been documented in Arachis. Here, we identified 381 de novo genes in A. hypogaea cv. Tifrunner based on comparison with five closely related Arachis species. There are distinct differences in gene expression patterns and gene structures between conserved and de novo genes. The identified de novo genes originated from ancestral sequence regions associated with metabolic and biosynthetic processes, and they were subsequently integrated into existing regulatory networks. De novo paralogs and homoeologs were identified in A. hypogaea cv. Tifrunner. De novo paralogs and homoeologs with conserved expression have mismatching cis-acting elements under normal growth conditions. De novo genes potentially have pluripotent functions in responses to biotic stresses as well as in growth and development based on quantitative trait locus data. This work provides a foundation for future research examining gene birth processes and gene function in Arachis and related taxa.
Collapse
Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Zhonglong Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Xiaojun Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Jiongming Sui
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
6
|
Li L, Cui S, Dang P, Yang X, Wei X, Chen K, Liu L, Chen CY. GWAS and bulked segregant analysis reveal the Loci controlling growth habit-related traits in cultivated Peanut (Arachis hypogaea L.). BMC Genomics 2022; 23:403. [PMID: 35624420 PMCID: PMC9145184 DOI: 10.1186/s12864-022-08640-3] [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: 06/09/2021] [Accepted: 05/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background Peanut (Arachis hypogaea L.) is a grain legume crop that originated from South America and is now grown around the world. Peanut growth habit affects the variety’s adaptability, planting patterns, mechanized harvesting, disease resistance, and yield. The objective of this study was to map the quantitative trait locus (QTL) associated with peanut growth habit-related traits by combining the genome-wide association analysis (GWAS) and bulked segregant analysis sequencing (BSA-seq) methods. Results GWAS was performed with 17,223 single nucleotide polymorphisms (SNPs) in 103 accessions of the U.S. mini core collection genotyped using an Affymetrix version 2.0 SNP array. With a total of 12,342 high-quality polymorphic SNPs, the 90 suggestive and significant SNPs associated with lateral branch angle (LBA), main stem height (MSH), lateral branch height (LBL), extent radius (ER), and the index of plant type (IOPT) were identified. These SNPs were distributed among 15 chromosomes. A total of 597 associated candidate genes may have important roles in biological processes, hormone signaling, growth, and development. BSA-seq coupled with specific length amplified fragment sequencing (SLAF-seq) method was used to find the association with LBA, an important trait of the peanut growth habit. A 4.08 Mb genomic region on B05 was associated with LBA. Based on the linkage disequilibrium (LD) decay distance, we narrowed down and confirmed the region within the 160 kb region (144,193,467–144,513,467) on B05. Four candidate genes in this region were involved in plant growth. The expression levels of Araip.E64SW detected by qRT-PCR showed significant difference between ‘Jihua 5’ and ‘M130’. Conclusions In this study, the SNP (AX-147,251,085 and AX-144,353,467) associated with LBA by GWAS was overlapped with the results in BSA-seq through combined analysis of GWAS and BSA-seq. Based on LD decay distance, the genome range related to LBA on B05 was shortened to 144,193,467–144,513,467. Three candidate genes related to F-box family proteins (Araip.E64SW, Araip.YG1LK, and Araip.JJ6RA) and one candidate gene related to PPP family proteins (Araip.YU281) may be involved in plant growth and development in this genome region. The expression analysis revealed that Araip.E64SW was involved in peanut growth habits. These candidate genes will provide molecular targets in marker-assisted selection for peanut growth habits. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08640-3.
Collapse
Affiliation(s)
- Li Li
- State Key Laboratory for Crop Improvement and Regulation in North China, College of Agronomy, Hebei Agricultural University, Baoding, 071001, The People's Republic of China.,Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36948, USA.,School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, The People's Republic of China
| | - Shunli Cui
- State Key Laboratory for Crop Improvement and Regulation in North China, College of Agronomy, Hebei Agricultural University, Baoding, 071001, The People's Republic of China
| | - Phat Dang
- USDA-ARS National Peanut Research Laboratory, Dawson, GA, 39842, USA
| | - Xinlei Yang
- State Key Laboratory for Crop Improvement and Regulation in North China, College of Agronomy, Hebei Agricultural University, Baoding, 071001, The People's Republic of China
| | - Xuejun Wei
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, The People's Republic of China
| | - Kai Chen
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, The People's Republic of China
| | - Lifeng Liu
- State Key Laboratory for Crop Improvement and Regulation in North China, College of Agronomy, Hebei Agricultural University, Baoding, 071001, The People's Republic of China.
| | - Charles Y Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36948, USA.
| |
Collapse
|
7
|
Ahmad N, Hou L, Ma J, Zhou X, Xia H, Wang M, Leal-Bertioli S, Zhao S, Tian R, Pan J, Li C, Li A, Bertioli D, Wang X, Zhao C. Bulk RNA-Seq Analysis Reveals Differentially Expressed Genes Associated with Lateral Branch Angle in Peanut. Genes (Basel) 2022; 13:genes13050841. [PMID: 35627225 PMCID: PMC9140427 DOI: 10.3390/genes13050841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/01/2022] [Accepted: 05/05/2022] [Indexed: 11/28/2022] Open
Abstract
Lateral branch angle (LBA), or branch habit, is one of the most important agronomic traits in peanut. To date, the underlying molecular mechanisms of LBA have not been elucidated in peanut. To acquire the differentially expressed genes (DEGs) related to LBA, a TI population was constructed through the hybridization of a bunch-type peanut variety Tifrunner and prostrate-type Ipadur. We report the identification of DEGs related to LBA by sequencing two RNA pools, which were composed of 45 F3 lines showing an extreme opposite bunch and prostrate phenotype. We propose to name this approach Bulk RNA-sequencing (BR-seq) as applied to several plant species. Through BR-seq analysis, a total of 3083 differentially expressed genes (DEGs) were identified, including 13 gravitropism-related DEGs, 22 plant hormone-related DEGs, and 55 transcription factors-encoding DEGs. Furthermore, we also identified commonly expressed alternatively spliced (AS) transcripts, of which skipped exon (SE) and retained intron (RI) were most abundant in the prostrate and bunch-type peanut. AS isoforms between prostrate and bunch peanut highlighted important clues to further understand the post-transcriptional regulatory mechanisms of branch angle regulation. Our findings provide not only important insights into the landscape of the regulatory pathway involved in branch angle formation but also present practical information for peanut molecular breeding in the future.
Collapse
Affiliation(s)
- Naveed Ahmad
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (N.A.); (L.H.); (J.M.); (H.X.); (S.Z.); (R.T.); (J.P.); (C.L.); (A.L.); (X.W.)
| | - Lei Hou
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (N.A.); (L.H.); (J.M.); (H.X.); (S.Z.); (R.T.); (J.P.); (C.L.); (A.L.); (X.W.)
- College of Life Sciences, Shandong Normal University, Jinan 250014, China; (X.Z.); (M.W.)
| | - Junjie Ma
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (N.A.); (L.H.); (J.M.); (H.X.); (S.Z.); (R.T.); (J.P.); (C.L.); (A.L.); (X.W.)
| | - Ximeng Zhou
- College of Life Sciences, Shandong Normal University, Jinan 250014, China; (X.Z.); (M.W.)
| | - Han Xia
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (N.A.); (L.H.); (J.M.); (H.X.); (S.Z.); (R.T.); (J.P.); (C.L.); (A.L.); (X.W.)
| | - Mingxiao Wang
- College of Life Sciences, Shandong Normal University, Jinan 250014, China; (X.Z.); (M.W.)
| | - Soraya Leal-Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA; (S.L.-B.); (D.B.)
- Department of Plant Pathology, University of Georgia, Athens, GA 31793, USA
| | - Shuzhen Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (N.A.); (L.H.); (J.M.); (H.X.); (S.Z.); (R.T.); (J.P.); (C.L.); (A.L.); (X.W.)
| | - Ruizheng Tian
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (N.A.); (L.H.); (J.M.); (H.X.); (S.Z.); (R.T.); (J.P.); (C.L.); (A.L.); (X.W.)
| | - Jiaowen Pan
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (N.A.); (L.H.); (J.M.); (H.X.); (S.Z.); (R.T.); (J.P.); (C.L.); (A.L.); (X.W.)
| | - Changsheng Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (N.A.); (L.H.); (J.M.); (H.X.); (S.Z.); (R.T.); (J.P.); (C.L.); (A.L.); (X.W.)
| | - Aiqin Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (N.A.); (L.H.); (J.M.); (H.X.); (S.Z.); (R.T.); (J.P.); (C.L.); (A.L.); (X.W.)
| | - David Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA; (S.L.-B.); (D.B.)
- Department of Crop and Soil Science, University of Georgia, Athens, GA 30602, USA
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (N.A.); (L.H.); (J.M.); (H.X.); (S.Z.); (R.T.); (J.P.); (C.L.); (A.L.); (X.W.)
- College of Life Sciences, Shandong Normal University, Jinan 250014, China; (X.Z.); (M.W.)
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China; (N.A.); (L.H.); (J.M.); (H.X.); (S.Z.); (R.T.); (J.P.); (C.L.); (A.L.); (X.W.)
- College of Life Sciences, Shandong Normal University, Jinan 250014, China; (X.Z.); (M.W.)
- Correspondence:
| |
Collapse
|
8
|
Sarkar S, Cazenave AB, Oakes J, McCall D, Thomason W, Abbott L, Balota M. Aerial high-throughput phenotyping of peanut leaf area index and lateral growth. Sci Rep 2021; 11:21661. [PMID: 34737338 PMCID: PMC8569151 DOI: 10.1038/s41598-021-00936-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/19/2021] [Indexed: 11/10/2022] Open
Abstract
Leaf area index (LAI) is the ratio of the total one-sided leaf area to the ground area, whereas lateral growth (LG) is the measure of canopy expansion. They are indicators for light capture, plant growth, and yield. Although LAI and LG can be directly measured, this is time consuming. Healthy leaves absorb in the blue and red, and reflect in the green regions of the electromagnetic spectrum. Aerial high-throughput phenotyping (HTP) may enable rapid acquisition of LAI and LG from leaf reflectance in these regions. In this paper, we report novel models to estimate peanut (Arachis hypogaea L.) LAI and LG from vegetation indices (VIs) derived relatively fast and inexpensively from the red, green, and blue (RGB) leaf reflectance collected with an unmanned aerial vehicle (UAV). In addition, we evaluate the models' suitability to identify phenotypic variation for LAI and LG and predict pod yield from early season estimated LAI and LG. The study included 18 peanut genotypes for model training in 2017, and 8 genotypes for model validation in 2019. The VIs included the blue green index (BGI), red-green ratio (RGR), normalized plant pigment ratio (NPPR), normalized green red difference index (NGRDI), normalized chlorophyll pigment index (NCPI), and plant pigment ratio (PPR). The models used multiple linear and artificial neural network (ANN) regression, and their predictive accuracy ranged from 84 to 97%, depending on the VIs combinations used in the models. The results concluded that the new models were time- and cost-effective for estimation of LAI and LG, and accessible for use in phenotypic selection of peanuts with desirable LAI, LG and pod yield.
Collapse
Affiliation(s)
- Sayantan Sarkar
- West Tennessee AgResearch and Education Center, Jackson, TN, USA
| | | | - Joseph Oakes
- Virginia Tech Eastern Virginia AREC, Warsaw, VA, USA
| | - David McCall
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Wade Thomason
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Lynn Abbott
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Maria Balota
- School of Plant and Environmental Sciences, Virginia Tech Tidewater AREC, Suffolk, VA, USA.
| |
Collapse
|
9
|
Mehnaz M, Dracatos P, Pham A, March T, Maurer A, Pillen K, Forrest K, Kulkarni T, Pourkheirandish M, Park RF, Singh D. Discovery and fine mapping of Rph28: a new gene conferring resistance to Puccinia hordei from wild barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2167-2179. [PMID: 33774682 DOI: 10.1007/s00122-021-03814-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
A new gene Rph28 conferring resistance to barley leaf rust was discovered and fine-mapped on chromosome 5H from wild barley. Leaf rust is a highly destructive disease of barley caused by the fungal pathogen Puccinia hordei. Genetic resistance is considered to be the most effective, economical and eco-friendly approach to minimize losses caused by this disease. A study was undertaken to characterize and fine map a seedling resistance gene identified in a Hordeum vulgare ssp. spontaneum-derived barley line, HEB-04-101, that is broadly effective against a diverse set of Australian P. hordei pathotypes. Genetic analysis of an F3 population derived from a cross between HEB-04-101 and the H. vulgare cultivar Flagship (seedling susceptible) confirmed the presence of a single dominant gene for resistance in HEB-04-101. Selective genotyping was performed on representative plants from non-segregating homozygous resistant and homozygous susceptible F3 families using the targeted genotyping-by-sequencing (tGBS) assay. Putatively linked SNP markers with complete fixation were identified on the long arm of chromosome 5H spanning a physical interval between 622 and 669 Mb based on the 2017 Morex barley reference genome assembly. Several CAPS (cleaved amplified polymorphic sequences) markers were designed from the pseudomolecule sequence of the Morex assembly (v1.0 and v2.0), and 16 polymorphic markers were able to delineate the RphHEB locus to a 0.05 cM genetic interval spanning 98.6 kb. Based on its effectiveness and wild origin, RphHEB is distinct from all other designated Rph genes located on chromosome 5H and therefore the new locus symbol Rph28 is recommended for RphHEB in accordance with the rules and cataloguing system of barley gene nomenclature.
Collapse
Affiliation(s)
- M Mehnaz
- Plant Breeding Institute Cobbitty, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia
| | - P Dracatos
- Plant Breeding Institute Cobbitty, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia
| | - A Pham
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - T March
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - A Maurer
- Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120, Halle/Saale, Germany
| | - K Pillen
- Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120, Halle/Saale, Germany
| | - K Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, 3083, Australia
| | - T Kulkarni
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, 3083, Australia
| | - M Pourkheirandish
- Faculty of Veterinary and Agriculture, The University of Melbourne, Parkville, 3010, Australia
| | - R F Park
- Plant Breeding Institute Cobbitty, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia
| | - D Singh
- Plant Breeding Institute Cobbitty, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia.
| |
Collapse
|
10
|
Kunta S, Agmon S, Chedvat I, Levy Y, Chu Y, Ozias-Akins P, Hovav R. Identification of consistent QTL for time to maturation in Virginia-type Peanut (Arachis hypogaea L.). BMC PLANT BIOLOGY 2021; 21:186. [PMID: 33874903 PMCID: PMC8054412 DOI: 10.1186/s12870-021-02951-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/29/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Time-to-maturation (TTM) is an important trait contributing to adaptability, yield and quality in peanut (Arachis hypogaea L). Virginia market-type peanut belongs to the late-maturing A. hypogaea subspecies with considerable variation in TTM within this market type. Consequently, planting and harvesting schedule of peanut cultivars, including Virginia market-type, need to be optimized to maximize yield and grade. Little is known regarding the genetic control of TTM in peanut due to the challenge of phenotyping and limited DNA polymorphism. Here, we investigated the genetic control of TTM within the Virginia market-type peanut using a SNP-based high-density genetic map. A recombinant inbred line (RIL) population, derived from a cross between two Virginia-type cultivars 'Hanoch' and 'Harari' with contrasting TTM (12-15 days on multi-years observations), was phenotyped in the field for 2 years following a randomized complete block design. TTM was estimated by maturity index (MI). Other agronomic traits like harvest index (HI), branching habit (BH) and shelling percentage (SP) were recorded as well. RESULTS MI was highly segregated in the population, with 13.3-70.9% and 28.4-80.2% in years 2018 and 2019. The constructed genetic map included 1833 SNP markers distributed on 24 linkage groups, covering a total map distance of 1773.5 cM corresponding to 20 chromosomes on the tetraploid peanut genome with 1.6 cM mean distance between the adjacent markers. Thirty QTL were identified for all measured traits. Among the four QTL regions for MI, two consistent QTL regions (qMIA04a,b and qMIB03a,b) were identified on chromosomes A04 (118680323-125,599,371; 6.9Mbp) and B03 (2839591-4,674,238; 1.8Mbp), with LOD values of 5.33-6.45 and 5-5.35 which explained phenotypic variation of 9.9-11.9% and 9.3-9.9%, respectively. QTL for HI were found to share the same loci as MI on chromosomes B03, B05, and B06, demonstrating the possible pleiotropic effect of HI on TTM. Significant but smaller effects on MI were detected for BH, pod yield and SP. CONCLUSIONS This study identified consistent QTL regions conditioning TTM for Virginia market-type peanut. The information and materials generated here can be used to further develop molecular markers to select peanut idiotypes suitable for diverse growth environments.
Collapse
Affiliation(s)
- Srinivas Kunta
- Department of Field Crops, Agriculture Research Organization-The Volcani Center, Institute of Plant Sciences, HaMakkabbim Road, P. O. Box 15159, 7505101, Rishon LeZiyyon, Israel
- Faculty of Agricultural, Food and The Environmental Quality Sciences, The Hebrew University of Jerusalem, POB 12, 76100, Rehovot, Israel
| | - Sara Agmon
- Department of Field Crops, Agriculture Research Organization-The Volcani Center, Institute of Plant Sciences, HaMakkabbim Road, P. O. Box 15159, 7505101, Rishon LeZiyyon, Israel
| | - Ilan Chedvat
- Department of Field Crops, Agriculture Research Organization-The Volcani Center, Institute of Plant Sciences, HaMakkabbim Road, P. O. Box 15159, 7505101, Rishon LeZiyyon, Israel
| | - Yael Levy
- Department of Field Crops, Agriculture Research Organization-The Volcani Center, Institute of Plant Sciences, HaMakkabbim Road, P. O. Box 15159, 7505101, Rishon LeZiyyon, Israel
| | - Ye Chu
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, 31793, USA
| | - Peggy Ozias-Akins
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, 31793, USA
| | - Ran Hovav
- Department of Field Crops, Agriculture Research Organization-The Volcani Center, Institute of Plant Sciences, HaMakkabbim Road, P. O. Box 15159, 7505101, Rishon LeZiyyon, Israel.
| |
Collapse
|
11
|
Zhang R, Ren Y, Wu H, Yang Y, Yuan M, Liang H, Zhang C. Mapping of Genetic Locus for Leaf Trichome Formation in Chinese Cabbage Based on Bulked Segregant Analysis. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10040771. [PMID: 33919922 PMCID: PMC8070908 DOI: 10.3390/plants10040771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
Chinese cabbage is a leafy vegetable, and its leaves are the main edible organs. The formation of trichomes on the leaves can significantly affect its taste, so studying this phenomenon is of great significance for improving the quality of Chinese cabbage. In this study, two varieties of Chinese cabbage, W30 with trichome leaves and 082 with glabrous leaves, were crossed to generate F1 and F1 plants, which were self-fertilized to develop segregating populations with trichome or glabrous morphotypes. The two bulks of the different segregating populations were used to conduct bulked segregant analysis (BSA). A total of 293.4 M clean reads were generated from the samples, and plants from the trichome leaves (AL) bulk and glabrous leaves (GL) bulk were identified. Between the two DNA pools generated from the trichome and glabrous plants, 55,048 SNPs and 272 indels were generated. In this study, three regions (on chromosomes 6, 10 and scaffold000100) were identified, and the annotation revealed three candidate genes that may participate in the formation of leaf trichomes. These findings suggest that the three genes-Bra025087 encoding a cyclin family protein, Bra035000 encoding an ATP-binding protein/kinase/protein kinase/protein serine/threonine kinase and Bra033370 encoding a WD-40 repeat family protein-influence the formation of trichomes by participating in trichome morphogenesis (GO: 0010090). These results demonstrate that BSA can be used to map genes associated with traits and provide new insights into the molecular mechanism of leafy trichome formation in Chinese cabbage.
Collapse
|
12
|
Physical mapping and InDel marker development for the restorer gene Rf 2 in cytoplasmic male sterile CMS-D8 cotton. BMC Genomics 2021; 22:24. [PMID: 33407111 PMCID: PMC7789476 DOI: 10.1186/s12864-020-07342-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 12/22/2020] [Indexed: 11/23/2022] Open
Abstract
Background Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 containing Rf2 gene can restore the fertility of the corresponding sterile line. This study combined the whole genome resequencing bulked segregant analysis (BSA) with high-throughput SNP genotyping to accelerate the physical mapping of Rf2 locus in CMS-D8 cotton. Methods The fertility of backcross population ((sterile line×restorer line)×maintainer line) comprising of 1623 individuals was investigated in the field. The fertile pool (100 plants with fertile phenotypes, F-pool) and the sterile pool (100 plants with sterile phenotypes, S-pool) were constructed for BSA resequencing. The selection of 24 single nucleotide polymorphisms (SNP) through high-throughput genotyping and the development insertion and deletion (InDel) markers were conducted to narrow down the candidate interval. The pentapeptide repeat (PPR) family genes and upregulated genes in restore line in the candidate interval were analysed by qRT-PCR. Results The fertility investigation results showed that fertile and sterile separation ratio was consistent with 1:1. BSA resequencing technology, high-throughput SNP genotyping, and InDel markers were used to identify Rf2 locus on candidate interval of 1.48 Mb on chromosome D05. Furthermore, it was quantified in this experiment that InDel markers co-segregated with Rf2 enhanced the selection of the restorer line. The qRT-PCR analysis revealed PPR family gene Gh_D05G3391 located in candidate interval had significantly lower expression than sterile and maintainer lines. In addition, utilization of anther RNA-Seq data of CMS-D8 identified that the expression level of Gh_D05G3374 encoding NB-ARC domain-containing disease resistance protein in restorer lines was significantly higher than that in sterile and maintainer lines. Conclusions This study not only enabled us to precisely locate the restore gene Rf2 but also evaluated the utilization of InDel markers for marker assisted selection in the CMS-D8 Rf2 cotton breeding line. The results of this study provide an important foundation for further studies on the mapping and cloning of restorer genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07342-y.
Collapse
|
13
|
Wang S, Zhang R, Shi Z, Zhao Y, Su A, Wang Y, Xing J, Ge J, Li C, Wang X, Wang J, Sun X, Liu Q, Chen Y, Zhang Y, Wang S, Song W, Zhao J. Identification and Fine Mapping of RppM, a Southern Corn Rust Resistance Gene in Maize. FRONTIERS IN PLANT SCIENCE 2020; 11:1057. [PMID: 32733529 PMCID: PMC7363983 DOI: 10.3389/fpls.2020.01057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/26/2020] [Indexed: 05/26/2023]
Abstract
Southern corn rust (SCR) caused by Puccinia polysora Underw. is a major disease causing severe yield losses during maize production. Here, we identified and mapped the SCR resistance gene RppM from the near-isogenic line Kangxiujing2416 (Jing2416K), which harbors RppM in the genetic background of the susceptible inbred line Jing2416. In this study, the inheritance of SCR resistance was investigated in F2 and F3 populations derived from a cross between Jing2416K and Jing2416. The observed 3:1 segregation ratio of resistant to susceptible plants indicated that the SCR resistance is controlled by a single dominant gene. Using an F2 population, we performed bulked segregant analysis (BSA) sequencing and mapped RppM to a 3.69-Mb region on chromosome arm 10S. To further narrow down the region harboring RppM, we developed 13 insertion/deletion (InDel) markers based on the sequencing data. Finally, RppM was mapped to a region spanning 110-kb using susceptible individuals from a large F2 population. Two genes (Zm00001d023265 and Zm00001d023267) encoding putative CC-NBS-LRR (coiled-coiled, nucleotide-binding site, and leucine-rich repeat) proteins, a common characteristic of R genes, were located in this region (B73 RefGen_v4 reference genome). Sequencing and comparison of the two genes cloned from Jing2416K and Jing2416 revealed sequence variations in their coding regions. The relative expression levels of these two genes in Jing2416K were found to be significantly higher than those in Jing2416. Zm00001d023265 and Zm00001d023267 are thus potential RppM candidates.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wei Song
- Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing, China
| | - Jiuran Zhao
- Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing, China
| |
Collapse
|
14
|
Yu X, Wang L, Xu K, Kong F, Wang D, Tang X, Sun B, Mao Y. Fine Mapping to Identify the Functional Genetic Locus for Red Coloration in Pyropia yezoensis Thallus. FRONTIERS IN PLANT SCIENCE 2020; 11:867. [PMID: 32655600 PMCID: PMC7324768 DOI: 10.3389/fpls.2020.00867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/27/2020] [Indexed: 05/26/2023]
Abstract
Pyropia yezoensis, commonly known as "Nori" or "Laver" is an economically important marine crop. In natural or selected populations of P. yezoensis, coloration mutants are frequently observed. Various coloration mutants are excellent materials for genetic research and study photosynthesis. However, the candidate gene controlling the Pyropia coloration phenotype remains unclear to date. QTL-seq, in combination with kompetitive allele-specific PCR (KASP) and RNA-seq, can be generally applied to population genomics studies to rapidly identify genes that are responsible for phenotypes showing extremely opposite traits. Through cross experiments between the wild line RZ and red-mutant HT, offsprings with 1-4 sectors chimeric blade were generated. Statistical analyses revealed that the red thallus coloration phenotype is conferred by a single nuclear allele. Two-pair populations, consisting of 24 and 56 wild-type/red-type single-genotype sectors from F1 progeny, were used in QTL-seq to detect a genomic region in P. yezoensis harboring the red coloration locus. Based on a high-quality genome, we first identified the candidate region within a 3.30-Mb region at the end of chromosome 1. Linkage map-based QTL analysis was used to confirm the candidate region identified by QTL-seq. Then, four KASP markers developed in this region were used to narrow down the candidate region to a 1.42-Mb region. Finally, we conducted RNA-seq to focus on 13 differentially expressed genes and further predicted rcl-1, which contains one non-synonymous SNP [A/C] in the coding region that could be regulating red thallus coloration in P. yezoensis. Our results provide novel insights into the underlying mechanism controlling blade coloration, which is a desirable trait in algae.
Collapse
Affiliation(s)
- Xinzi Yu
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lu Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Kuipeng Xu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Fanna Kong
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Dongmei Wang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xianghai Tang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Bin Sun
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunxiang Mao
- Key Laboratory of Utilization and Conservation of Tropical Marine Bioresource (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
| |
Collapse
|
15
|
Mondal S, Badigannavar AM. Identification of major consensus QTLs for seed size and minor QTLs for pod traits in cultivated groundnut ( Arachis hypogaea L.). 3 Biotech 2019; 9:347. [PMID: 31497465 DOI: 10.1007/s13205-019-1881-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/22/2019] [Indexed: 12/16/2022] Open
Abstract
Hundred kernel weight is an important indicator for large-seeded genotype selection. A recombinant inbred line population was used to decipher the genetic architecture of seed size and three pod traits in cultivated groundnut based on the phenotypic data from six and three environments, respectively. The study revealed a consensus major QTL for HKW in B07 group that explained 10.5-23.9% phenotypic variation due to seed size. Further, two other minor QTLs were identified in B03 and B08 group for the seed size. Two minor QTLs for pod beak were positioned in B03 and A08. A minor QTL for pod reticulation was also mapped in the same map interval with the pod beak QTL in A08. Another minor QTL for pod constriction was co-mapped with the minor QTL for HKW in B08. The other minor QTL for pod constriction was placed in the neighboring map interval with the consensus QTL for seed size in B07 that suggests linkage of pod constriction with large seed trait. Analysis of the flanking markers profile in 71 cultivated groundnut genotypes revealed a strong association of pPGPseq_2E06 marker with large seed trait.
Collapse
Affiliation(s)
- Suvendu Mondal
- 1Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- 2Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094 India
| | - Anand M Badigannavar
- 1Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- 2Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094 India
| |
Collapse
|
16
|
Liu G, Zhao T, You X, Jiang J, Li J, Xu X. Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum). BMC PLANT BIOLOGY 2019; 19:15. [PMID: 30621598 PMCID: PMC6325758 DOI: 10.1186/s12870-018-1616-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/21/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Leaf mold, one of the major diseases of tomato caused by Cladosporium fulvum (C. fulvum), can dramatically reduce the yield and cause multimillion dollar losses annually worldwide. Mapping the resistance genes (R genes) of C. fulvum and devising MAS based strategies for breeding new cultivars is an effective approach to improve the resistance in tomato. Up to now, many C. fulvum genes or QTLs have been mapped using different genetic materials, but few studies focused on Cf-10 gene positioning. RESULTS In this study, we investigated the genetic rules for Cf-10 and used a novel combinatorial strategy to rapidly map the Cf-10 gene. Initially, the performance of F1, F2 and BC1F1 individuals after infection, demonstrated that the resistance against C. fulvum was controlled by a single dominant gene. Two pools of resistant and susceptible individuals from F2 population were investigated, using mapping by sequencing approach and Cf-10 was found to be localized to 3.35 Mb and 3.74 Mb on chromosome 1, employing SNP/InDel index methods, respectively. After accounting for overlapping regions, these two algorithms yielded a total length of 3.29 Mb, narrowing down the target region. We further developed five serviceable KASP markers for this region based on sequencing data and conducted local QTL mapping using individuals from the F2 population, except for mapping by sequencing as mentioned above. Finally Cf-10 gene was mapped spanning a region of 790 kb, where only one gene (Solyc01g007130.3) was annotated as probable receptor protein kinase TMK1 with a LRR motif, a common R gene characteristic. The RT-qPCR analysis further confirmed the localization and the relative expression of Solyc01g007130.3 in Ontario 792 and was found to be significantly higher than that in Moneymaker at 9 dpi and 12 dpi, respectively. CONCLUSION This study proposed a novel combinatorial strategy by combining SNP-index, InDel-index analyses and local QTL mapping using KASP genotyping approach to rapidly map genes responsible for specific traits and provided a robust base for cloning the Cf-10 gene. Furthermore, these analyses suggest that Solyc01g007130.3 is a potential candidate to be regarded as Cf-10 gene.
Collapse
Affiliation(s)
- Guan Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030 China
| | - Tingting Zhao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030 China
| | - Xiaoqing You
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030 China
| | - Jingbin Jiang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030 China
| | - Jingfu Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030 China
| | - Xiangyang Xu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030 China
| |
Collapse
|
17
|
Li L, Yang X, Cui S, Meng X, Mu G, Hou M, He M, Zhang H, Liu L, Chen CY. Construction of High-Density Genetic Map and Mapping Quantitative Trait Loci for Growth Habit-Related Traits of Peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2019; 10:745. [PMID: 31263472 PMCID: PMC6584813 DOI: 10.3389/fpls.2019.00745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/20/2019] [Indexed: 05/03/2023]
Abstract
Plant growth habit is an important and complex agronomic trait and is associated with yield, disease resistance, and mechanized harvesting in peanuts. There are at least two distinct growth habits (erect and prostrate) and several intermediate forms existing in the peanut germplasm. A recombinant inbred line population containing 188 individuals was developed from a cross of "Jihua 5" and "M130" for genetically dissecting the architecture of the growth habit. A new high-density genetic linkage map was constructed by using specific locus amplified fragment sequencing technology. The map contains 2,808 single-nucleotide polymorphism markers distributed on 20 linkage groups with a total length of 1,308.20 cM and an average inter-marker distance of 0.47 cM. The quantitative trait locus (QTL) analysis of the growth habit-related traits was conducted based on phenotyping data from seven environments. A total of 39 QTLs for growth habit-related traits was detected on 10 chromosomes explaining 4.55-27.74% of the phenotypic variance, in which 6 QTLs were for lateral branch angle, 8 QTLs were for extent radius, 7 QTLs were for the index of plant type, 11 QTLs were for main stem height, and 7 QTLs were for lateral branch length. Among these QTLs, 12 were co-localized on chromosome B05 spanning an approximately 0.17 Mb physical interval in comparison with the allotetraploid reference genome of "Tifrunner." Analysis of the co-localized genome region has shown that the putative genes are involved in light and hormones and will facilitate peanut growth habit molecular breeding and study of peanut domestication.
Collapse
Affiliation(s)
- Li Li
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Xinlei Yang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Shunli Cui
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xinhao Meng
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Guojun Mu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Mingyu Hou
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Meijing He
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Hui Zhang
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Lifeng Liu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
- *Correspondence: Lifeng Liu,
| | - Charles Y. Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
- Charles Y. Chen,
| |
Collapse
|
18
|
Patil AS, Popovsky S, Levy Y, Chu Y, Clevenger J, Ozias-Akins P, Hovav R. Genetic insight and mapping of the pod constriction trait in Virginia-type peanut. BMC Genet 2018; 19:93. [PMID: 30340455 PMCID: PMC6195699 DOI: 10.1186/s12863-018-0674-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/13/2018] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Pod constriction is an important descriptive and agronomic trait of peanut. For the in-shell Virginia marketing-type, this trait has commercial importance as well, since deeply constricted pods have a tendency to break, which makes them unmarketable. Classical genetic studies have indicated that pod constriction in peanut is controlled by one to four genes, depending on the genetic background. In all of those studies, pod constriction was evaluated visually as opposed to quantitatively. Here, we examined the genetic nature of this trait in the Virginia-type background. Our study involved 195 recombinant inbred lines (F7RILs) derived from two closely related cultivars that differ in their degree of pod constriction. Pod constriction was evaluated visually and quantitatively in terms of the pod constriction index (PCI), calculated as the average ratio between the pod's waist and shoulders. RESULTS ANOVA and genetic parameters for PCI among the F7RILs in three blocks showed very significant genotypic effect (p(F) < 0.0001) and high heritability and genetic gain estimates (0.84 and 0.52, respectively). The mean PCI values of the different RILs had a bimodal distribution with an approximate 1:1 ratio between the two curves. Pod constriction was also determined visually (VPC) by grading the degree of each RIL as 'deep' or 'slight'. The χ2 test was found to not be significantly different from a 1:1 ratio (p = 0.79) as well. SNP-array-based technology was used to map this trait in the RIL population. A major locus for the pod constriction trait was found on chromosome B7, between B07_120,287,958 and B07_120,699,791, and the best-linked SNP explained 32% of the total variation within that region. Some discrepancy was found between the SNPs original location and the genetic mapping of the trait. CONCLUSION The trait distribution and mapping, together with data from F1 and F2 generations indicate that in this background the pod constriction is controlled by a major recessive gene. The identity of loci controlling the pod constriction trait will allow breeders to apply marker-assisted breeding approaches to shift allelic frequencies towards a slighter pod constriction and will facilitate future effort for map-based gene cloning.
Collapse
Affiliation(s)
- Abhinandan S. Patil
- Department of Field Crops, Institute of Plant Sciences, Agriculture research organization –the Volcani Center, HaMakkabbim Road, P. O. Box 15159, 7505101 Rishon LeZiyyon, Israel
| | - Sigal Popovsky
- Department of Field Crops, Institute of Plant Sciences, Agriculture research organization –the Volcani Center, HaMakkabbim Road, P. O. Box 15159, 7505101 Rishon LeZiyyon, Israel
| | - Yael Levy
- Department of Field Crops, Institute of Plant Sciences, Agriculture research organization –the Volcani Center, HaMakkabbim Road, P. O. Box 15159, 7505101 Rishon LeZiyyon, Israel
| | - Ye Chu
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, The University of Georgia, Tifton, GA 31793 USA
| | - Josh Clevenger
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, The University of Georgia, Tifton, GA 31793 USA
| | - Peggy Ozias-Akins
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, The University of Georgia, Tifton, GA 31793 USA
| | - Ran Hovav
- Department of Field Crops, Institute of Plant Sciences, Agriculture research organization –the Volcani Center, HaMakkabbim Road, P. O. Box 15159, 7505101 Rishon LeZiyyon, Israel
| |
Collapse
|
19
|
Chopra R, Simpson CE, Hillhouse A, Payton P, Sharma J, Burow MD. SNP genotyping reveals major QTLs for plant architectural traits between A-genome peanut wild species. Mol Genet Genomics 2018; 293:1477-1491. [PMID: 30069598 DOI: 10.1007/s00438-018-1472-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 07/09/2018] [Indexed: 12/19/2022]
Abstract
KEY MESSAGE QTL mapping of important architectural traits was successfully applied to an A-genome diploid population using gene-specific variations. Peanut wild species are an important source of resistance to biotic and possibly abiotic stress; because these species differ from the cultigen in many traits, we have undertaken to identify QTLs for several plant architecture-related traits. In this study, we took recently identified SNPs, converted them into markers, and identified QTLs for architectural traits. SNPs from RNASeq data distinguishing two parents, A. duranensis (KSSc38901) and A. cardenasii (GKP10017), of a mapping population were identified using three references-A. duranensis V14167 genome sequence, and transcriptome sequences of A. duranensis KSSc38901 and OLin. More than 49,000 SNPs differentiated the parents, and 87.9% of the 190 SNP calls tested were validated. SNPs were then genotyped on 91 F2 lines using KASP chemistry on a Roche LightCycler 480 and a Fluidigm Biomark HD, and using SNPType chemistry on the Fluidigm Biomark HD. A linkage map was constructed having ten linkage groups, with 144 loci spanning a total map distance of 1040 cM. Comparison of the A-genome map to the A. duranensis genome sequence revealed a high degree of synteny. QTL analysis was also performed on the mapping population for important architectural traits. Fifteen definitive and 16 putative QTLs for petiole length, leaflet length and width, leaflet area, leaflet length/width ratio, main stem height, presence of flowers on the main stem, and seed mass were identified. Results demonstrate that SNPs identified from transcriptome sequencing could be converted to KASP or SNPType markers with a high success rate, and used to identify alleles with significant phenotypic effects, These could serve as information useful for introgression of alleles into cultivated peanut from wild species and have the potential to allow breeders to more easily fix these alleles using a marker-assisted backcrossing approach.
Collapse
Affiliation(s)
- Ratan Chopra
- Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | | | - Andrew Hillhouse
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, 77843, USA
| | | | - Jyotsna Sharma
- Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Mark D Burow
- Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
- Texas A&M AgriLife Research, Lubbock, TX, 79403, USA.
| |
Collapse
|