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Schwertfirm G, Schneider M, Haase F, Riedel C, Lazzaro M, Ruge-Wehling B, Schweizer G. Genome-wide association study revealed significant SNPs for anthracnose resistance, seed alkaloids and protein content in white lupin. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:155. [PMID: 38858311 PMCID: PMC11164739 DOI: 10.1007/s00122-024-04665-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
White lupin (Lupinus albus L.) is a high-protein grain legume alternative to soybean in Central Europe, but its cultivation is risky due to the fungal disease anthracnose that can cause severe yield damage. In addition, management of seed alkaloids is critical for human nutrition and animal feed. We report on a white lupin collection of genebank accessions, advanced breeding lines and cultivars that was genotyped and phenotypically characterized for anthracnose resistance and seed alkaloids and protein levels. Using genotyping by sequencing (GBS), SeqSNP-targeted GBS, BiomarkX genotyping and Sanger sequencing, a genetic resource of genome-wide SNPs for white lupin was established. We determined anthracnose resistance in two years field trials at four locations with infection rows and measured seed alkaloids and protein levels by near-infrared spectroscopy (NIRS). Few white lupin breeding lines showed anthracnose resistance comparable or better than Celina and Frieda, currently the best commercial cultivars in Germany. NIRS estimates for seed alkaloids and protein levels revealed variation in the white lupin collection. Using genome-wide association studies (GWAS), we identified SNPs significantly associated with anthracnose resistance in the field representing known and new genomic regions. We confirmed the pauper locus and detected new SNP markers significantly associated with seed alkaloids. For the first time, we present loci associated with total grain protein content. Finally, we tested the potential of genomic prediction (GP) in predicting the phenotype of these three quantitative traits. Application of results and resources are discussed in the context of fostering breeding programs for white lupin.
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Affiliation(s)
- Grit Schwertfirm
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Am Gereuth 2, 85354, Freising, Germany.
| | - Michael Schneider
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, Box 219, 5070, Frick, Switzerland
| | - Florian Haase
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research On Agricultural Crops, Julius Kuehn-Institute (JKI), Rudolf Schick Platz 3a, 18190, Groß Lüsewitz, Germany
| | - Christine Riedel
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Kleeberg 14, 94099, Ruhstorf a. d. Rott, Germany
| | - Mariateresa Lazzaro
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, Box 219, 5070, Frick, Switzerland
| | - Brigitte Ruge-Wehling
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research On Agricultural Crops, Julius Kuehn-Institute (JKI), Rudolf Schick Platz 3a, 18190, Groß Lüsewitz, Germany
| | - Guenther Schweizer
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Am Gereuth 2, 85354, Freising, Germany
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Tam NT, Nhan DK. Identification of Insertion/Deletion Markers for Photoperiod Sensitivity in Rice ( Oryza sativa L.). BIOLOGY 2024; 13:358. [PMID: 38785840 PMCID: PMC11117668 DOI: 10.3390/biology13050358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/06/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
The current study aims to identify candidate insertion/deletion (INDEL) markers associated with photoperiod sensitivity (PS) in rice landraces from the Vietnamese Mekong Delta. The whole-genome sequencing of 20 accessions was conducted to analyze INDEL variations between two photoperiod-sensitivity groups. A total of 2240 INDELs were identified between the two photoperiod-sensitivity groups. The selection criteria included INDELs with insertions or deletions of at least 20 base pairs within the improved rice group. Six INDELs were discovered on chromosomes 01 (5 INDELs) and 6 (1 INDEL), and two genes were identified: LOC_Os01g23780 and LOC_Os01g36500. The gene LOC_Os01g23780, which may be involved in rice flowering, was identified in a 20 bp deletion on chromosome 01 from the improved rice accession group. A marker was devised for this gene, indicating a polymorphism rate of 20%. Remarkably, 20% of the materials comprised improved rice accessions. This INDEL marker could explain 100% of the observed distinctions. Further analysis of the mapping population demonstrated that an INDEL marker associated with the MADS-box gene on chromosome 01 was linked to photoperiod sensitivity. The F1 population displayed two bands across all hybrid individuals. The marker demonstrates efficacy in distinguishing improved rice accessions within the indica accessions. This study underscores the potential applicability of the INDEL marker in breeding strategies.
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Affiliation(s)
- Nguyen Thanh Tam
- Mekong Delta Development Research Institute, Can Tho University, Campus 2, 3-2 Street, Can Tho 94115, Vietnam
| | - Dang Kieu Nhan
- Mekong Delta Development Research Institute, Can Tho University, Campus 2, 3-2 Street, Can Tho 94115, Vietnam
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Yang F, Guo Y, Li J, Lu C, Wei Y, Gao J, Xie Q, Jin J, Zhu G. Genome-wide association analysis identified molecular markers and candidate genes for flower traits in Chinese orchid ( Cymbidium sinense). HORTICULTURE RESEARCH 2023; 10:uhad206. [PMID: 38046850 PMCID: PMC10689080 DOI: 10.1093/hr/uhad206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/07/2023] [Indexed: 12/05/2023]
Abstract
The orchid, the champagne of flowers, brings luxury, elegance, and novelty to nature. Cymbidium sinense is a symbol of gigantic floral variability on account of wavering shapes and sizes of floral organs, although marker-trait association (MTA) has not been studied for its floral traits. We evaluated markers associated with 14 floral traits of C. sinense through a genome-wide association study (GWAS) of 195 accessions. A total of 65 318 522 single-nucleotide polymorphisms (SNPs) and 3 906 176 insertion/deletion (InDel) events were identified through genotyping-by-sequencing. Among these, 4694 potential SNPs and 477 InDels were identified as MTAs at -log10 P > 5. The genes related to these SNPs and InDels were largely associated with floral regulators, hormonal pathways, cell division, and metabolism, playing essential roles in tailoring floral morphology. Moreover, 20 candidate SNPs/InDels linked to 11 genes were verified, 8 of which were situated on exons, one was located in the 5'-UTR and two were positioned in introns. Here, the multitepal trait-related gene RABBIT EARS (RBE) was found to be the most crucial gene. We analyzed the role of CsRBE in the regulation of flower-related genes via efficient transient overexpression in C. sinense protoplasts, and found that the floral homeotic genes CsAP3 and CsPI, as well as organ boundary regulators, including CsCUC and CsTCP genes, were regulated by CsRBE. Thus, we obtained key gene loci for important ornamental traits of orchids using genome-wide association analysis of populations with natural variation. The findings of this study can do a great deal to expedite orchid breeding programs for shape variability.
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Affiliation(s)
- Fengxi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yudi Guo
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jie Li
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chuqiao Lu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yonglu Wei
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jie Gao
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Qi Xie
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jianpeng Jin
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Genfa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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Su Y, Zhang M, Guo Q, Wei M, Shi H, Wang T, Han Z, Liu H, Liu C, Huang J. Classification of Isatis indigotica Fortune and Isatis tinctoria Linnaeus via comparative analysis of chloroplast genomes. BMC Genomics 2023; 24:465. [PMID: 37596543 PMCID: PMC10436401 DOI: 10.1186/s12864-023-09534-8] [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: 11/11/2022] [Accepted: 07/26/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND Isatis tinctoria Linnaeus and Isatis indigotica Fortune are very inconsistent in their morphological characteristics, but the Flora of China treats them as the same species. In this work, a new technology that differs from conventional barcodes is developed to prove that they are different species and to clarify their classification. RESULTS AND METHODS I. indigotica was indistinguishable from I. tinctoria when using ITS2. CPGAVAS2 was used to construct the chloroplast genomes. MAFFT and DnaSP were used to calculate nucleotide polymorphism, the chloroplast genomes of the two have high diversity in the rpl32 ~ trnL-UAG short region. When using this region as a mini barcode, it was found that there are obvious differences in the base numbers of I. tinctoria and different ploidy I. indigotica were found, but diploid and tetraploid I. indigotica had the same number of bases. Moreover, the reconstruction of the maximum likelihood (ML) tree, utilizing the mini-barcode, demonstrated that I. tinctoria and both diploid and tetraploid I. indigotica are located on distinct branches. The genome size of tetraploid I. indigotica was approximately 643.773 MB, the heterozygosity rate was approximately 0.98%, and the repeat sequence content was approximately 90.43%. This species has a highly heterozygous, extremely repetitive genome. CONCLUSION A new method was established to differentiate between I. indigotica and I. tinctoria. Furthermore, this approach provides a reference and basis for the directional breeding of Isatis.
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Grants
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
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Affiliation(s)
- Yong Su
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
| | - Man Zhang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
| | - Qiaosheng Guo
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China.
| | - Min Wei
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen City, 518000, PR China
| | - Hongzhuan Shi
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
| | - Tao Wang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
| | - Zhengzhou Han
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen City, 518000, PR China
| | - Huihui Liu
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen City, 518000, PR China
| | - Chang Liu
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
| | - Jianmin Huang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
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A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations. Sci Rep 2022; 12:17583. [PMID: 36266371 PMCID: PMC9584886 DOI: 10.1038/s41598-022-19858-2] [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: 09/20/2021] [Accepted: 09/06/2022] [Indexed: 01/13/2023] Open
Abstract
The development of next-generation sequencing (NGS) enabled a shift from array-based genotyping to directly sequencing genomic libraries for high-throughput genotyping. Even though whole-genome sequencing was initially too costly for routine analysis in large populations such as breeding or genetic studies, continued advancements in genome sequencing and bioinformatics have provided the opportunity to capitalize on whole-genome information. As new sequencing platforms can routinely provide high-quality sequencing data for sufficient genome coverage to genotype various breeding populations, a limitation comes in the time and cost of library construction when multiplexing a large number of samples. Here we describe a high-throughput whole-genome skim-sequencing (skim-seq) approach that can be utilized for a broad range of genotyping and genomic characterization. Using optimized low-volume Illumina Nextera chemistry, we developed a skim-seq method and combined up to 960 samples in one multiplex library using dual index barcoding. With the dual-index barcoding, the number of samples for multiplexing can be adjusted depending on the amount of data required, and could be extended to 3,072 samples or more. Panels of doubled haploid wheat lines (Triticum aestivum, CDC Stanley x CDC Landmark), wheat-barley (T. aestivum x Hordeum vulgare) and wheat-wheatgrass (Triticum durum x Thinopyrum intermedium) introgression lines as well as known monosomic wheat stocks were genotyped using the skim-seq approach. Bioinformatics pipelines were developed for various applications where sequencing coverage ranged from 1 × down to 0.01 × per sample. Using reference genomes, we detected chromosome dosage, identified aneuploidy, and karyotyped introgression lines from the skim-seq data. Leveraging the recent advancements in genome sequencing, skim-seq provides an effective and low-cost tool for routine genotyping and genetic analysis, which can track and identify introgressions and genomic regions of interest in genetics research and applied breeding programs.
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Chongtham SK, Devi EL, Samantara K, Yasin JK, Wani SH, Mukherjee S, Razzaq A, Bhupenchandra I, Jat AL, Singh LK, Kumar A. Orphan legumes: harnessing their potential for food, nutritional and health security through genetic approaches. PLANTA 2022; 256:24. [PMID: 35767119 DOI: 10.1007/s00425-022-03923-1] [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: 07/16/2021] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Legumes, being angiosperm's third-largest family as well as the second major crop family, contributes beyond 33% of human dietary proteins. The advent of the global food crisis owing to major climatic concerns leads to nutritional deprivation, hunger and hidden hunger especially in developing and underdeveloped nations. Hence, in the wake of promoting sustainable agriculture and nutritional security, apart from the popular legumes, the inclusion of lesser-known and understudied local crop legumes called orphan legumes in the farming systems of various tropical and sub-tropical parts of the world is indeed a need of the hour. Despite possessing tremendous potentialities, wide adaptability under diverse environmental conditions, and rich in nutritional and nutraceutical values, these species are still in a neglected and devalued state. Therefore, a major re-focusing of legume genetics, genomics, and biology is much crucial in pursuance of understanding the yield constraints, and endorsing underutilized legume breeding programs. Varying degrees of importance to these crops do exist among researchers of developing countries in establishing the role of orphan legumes as future crops. Under such circumstances, this article assembles a comprehensive note on the necessity of promoting these crops for further investigations and sustainable legume production, the exploitation of various orphan legume species and their potencies. In addition, an attempt has been made to highlight various novel genetic, molecular, and omics approaches for the improvement of such legumes for enhancing yield, minimizing the level of several anti-nutritional factors, and imparting biotic and abiotic stress tolerance. A significant genetic enhancement through extensive research in 'omics' areas is the absolute necessity to transform them into befitting candidates for large-scale popularization around the globe.
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Affiliation(s)
- Sunil Kumar Chongtham
- Multi Technology Testing Centre and Vocational Training Centre, CAEPHT, CAU, Ranipool, Gangtok, Sikkim, 737135, India
| | | | - Kajal Samantara
- Department of Genetics and Plant Breeding, Centurion University of Technology and Management, Odisha, 761211, India
| | - Jeshima Khan Yasin
- Division of Genomic Resources, ICAR-National Bureau Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani, Sher-E-Kashmir University of Agricultural Sciences and Technology, Srinagar, 192101, Jammu and Kashmir, India.
| | - Soumya Mukherjee
- Department of Botany, Jangipur College, University of Kalyani, West Bengal, 742213, India
| | - Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Ingudam Bhupenchandra
- ICAR-KVK Tamenglong, ICAR RC for NEH Region, Manipur Centre, Lamphelpat, Imphal, Manipur, 795 004, India
| | - Aanandi Lal Jat
- Castor-Mustard Research Station, SDAU, S.K. Nagar, Banaskantha, Gujarat, 385 506, India
| | - Laishram Kanta Singh
- ICAR-KVK Imphal West, ICAR RC for NEH region, Manipur Centre, Lamphelpat, Imphal, Manipur, 795 004, India
| | - Amit Kumar
- ICAR Research Complex for NEH Region, Tadong, Sikkim Centre, 737102, India
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Jiang X, Yang T, Zhang F, Yang X, Yang C, He F, Long R, Gao T, Jiang Y, Yang Q, Wang Z, Kang J. RAD-Seq-Based High-Density Linkage Maps Construction and Quantitative Trait Loci Mapping of Flowering Time Trait in Alfalfa ( Medicago sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:899681. [PMID: 35720570 PMCID: PMC9199863 DOI: 10.3389/fpls.2022.899681] [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: 03/19/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Alfalfa (Medicago sativa L.) is a perennial forage crop known as the "Queen of Forages." To dissect the genetic mechanism of flowering time (FT) in alfalfa, high-density linkage maps were constructed for both parents of an F1 mapping population derived from a cross between Cangzhou (P1) and ZhongmuNO.1 (P2), consisting of 150 progenies. The FT showed a transgressive segregation pattern in the mapping population. A total of 13,773 single-nucleotide polymorphism markers was obtained by using restriction-site associated DNA sequencing and distributed on 64 linkage groups, with a total length of 3,780.49 and 4,113.45 cM and an average marker interval of 0.58 and 0.59 cM for P1 and P2 parent, respectively. Quantitative trait loci (QTL) analyses were performed using the least square means of each year as well as the best linear unbiased prediction values across 4 years. Sixteen QTLs for FT were detected for P1 and 22 QTLs for P2, accounting for 1.40-16.04% of FT variation. RNA-Seq analysis at three flowering stages identified 5,039, 7,058, and 7,996 genes that were differentially expressed between two parents, respectively. Based on QTL mapping, DEGs analysis, and functional annotation, seven candidate genes associated with flowering time were finally detected. This study discovered QTLs and candidate genes for alfalfa FT, making it a useful resource for breeding studies on this essential crop.
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Affiliation(s)
- Xueqian Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianhui Yang
- Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, China
| | - Fan Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xijiang Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changfu Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fei He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ting Gao
- Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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A successful defense of the narrow-leafed lupin against anthracnose involves quick and orchestrated reprogramming of oxidation-reduction, photosynthesis and pathogenesis-related genes. Sci Rep 2022; 12:8164. [PMID: 35581248 PMCID: PMC9114385 DOI: 10.1038/s41598-022-12257-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/05/2022] [Indexed: 11/08/2022] Open
Abstract
Narrow-leafed lupin (NLL, Lupinus angustifolius L.) is a legume plant cultivated for grain production and soil improvement. Worldwide expansion of NLL as a crop attracted various pathogenic fungi, including Colletotrichum lupini causing a devastating disease, anthracnose. Two alleles conferring improved resistance, Lanr1 and AnMan, were exploited in NLL breeding, however, underlying molecular mechanisms remained unknown. In this study, European NLL germplasm was screened with Lanr1 and AnMan markers. Inoculation tests in controlled environment confirmed effectiveness of both resistance donors. Representative resistant and susceptible lines were subjected to differential gene expression profiling. Resistance to anthracnose was associated with overrepresentation of "GO:0006952 defense response", "GO:0055114 oxidation-reduction process" and "GO:0015979 photosynthesis" gene ontology terms. Moreover, the Lanr1 (83A:476) line revealed massive transcriptomic reprogramming quickly after inoculation, whereas other lines showed such a response delayed by about 42 h. Defense response was associated with upregulation of TIR-NBS, CC-NBS-LRR and NBS-LRR genes, pathogenesis-related 10 proteins, lipid transfer proteins, glucan endo-1,3-beta-glucosidases, glycine-rich cell wall proteins and genes from reactive oxygen species pathway. Early response of 83A:476, including orchestrated downregulation of photosynthesis-related genes, coincided with the successful defense during fungus biotrophic growth phase, indicating effector-triggered immunity. Mandelup response was delayed and resembled general horizontal resistance.
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Feng K, Kan XY, Li R, Yan YJ, Zhao SP, Wu P, Li LJ. Integrative Analysis of Long- and Short-Read Transcriptomes Identify the Regulation of Terpenoids Biosynthesis Under Shading Cultivation in Oenanthe javanica. Front Genet 2022; 13:813216. [PMID: 35464839 PMCID: PMC9022222 DOI: 10.3389/fgene.2022.813216] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Water dropwort (Oenanthe javanica) is a popular vegetable with high nutritional value and distinctive flavor. The flavor is mainly correlate with the biosynthesis of terpenoids. Shading cultivation was used to improve the flavor in the production of water dropwort. However, the changes of terpenoids and the genes involved in terpenoids biosynthesis under shading treatment remains unclear. In this study, the long- and short-reads transcriptomes of water dropwort were constructed. In total, 57,743 non-redundant high-quality transcripts were obtained from the transcriptome. 28,514 SSRs were identified from non-redundant transcripts and the mono-nucleotide repeats were the most abundant SSRs. The lncRNAs of water dropwort were recognized and their target genes were predicted. The volatile compound contents in petioles and leaf blades of water dropwort were decreased after the shading treatment. The DEGs analysis was performed to identify the terpenoids biosynthesis genes. The results indicated that 5,288 DEGs were differentially expressed in petiole, of which 22 DEGs were enriched in the terpenoids backbone biosynthesis pathway. A total of 12 DEGs in terpenoids biosynthesis pathway were selected and further verified by qRT-PCR assay, demonstrating that the terpenoids biosynthesis genes were down-regulated under shading treatment. Here, the full-length transcriptome was constructed and the regulatory genes related to terpenoids biosynthesis in water dropwort were also investigated. These results will provide useful information for future researches on functional genomics and terpenoids biosynthesis mechanism in water dropwort.
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Affiliation(s)
- Kai Feng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xia-Yue Kan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Rui Li
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Ya-Jie Yan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Shu-Ping Zhao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Peng Wu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Liang-Jun Li
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
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Jha UC, Nayyar H, Parida SK, Bakır M, von Wettberg EJB, Siddique KHM. Progress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era. Front Genet 2022; 13:831656. [PMID: 35464848 PMCID: PMC9021634 DOI: 10.3389/fgene.2022.831656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
Legume crops, belonging to the Fabaceae family, are of immense importance for sustaining global food security. Many legumes are profitable crops for smallholder farmers due to their unique ability to fix atmospheric nitrogen and their intrinsic ability to thrive on marginal land with minimum inputs and low cultivation costs. Recent progress in genomics shows promise for future genetic gains in major grain legumes. Still it remains limited in minor legumes/underutilized legumes, including adzuki bean, cluster bean, horse gram, lathyrus, red clover, urd bean, and winged bean. In the last decade, unprecedented progress in completing genome assemblies of various legume crops and resequencing efforts of large germplasm collections has helped to identify the underlying gene(s) for various traits of breeding importance for enhancing genetic gain and contributing to developing climate-resilient cultivars. This review discusses the progress of genomic resource development, including genome-wide molecular markers, key breakthroughs in genome sequencing, genetic linkage maps, and trait mapping for facilitating yield improvement in underutilized legumes. We focus on 1) the progress in genomic-assisted breeding, 2) the role of whole-genome resequencing, pangenomes for underpinning the novel genomic variants underlying trait gene(s), 3) how adaptive traits of wild underutilized legumes could be harnessed to develop climate-resilient cultivars, 4) the progress and status of functional genomics resources, deciphering the underlying trait candidate genes with putative function in underutilized legumes 5) and prospects of novel breeding technologies, such as speed breeding, genomic selection, and genome editing. We conclude the review by discussing the scope for genomic resources developed in underutilized legumes to enhance their production and play a critical role in achieving the "zero hunger" sustainable development goal by 2030 set by the United Nations.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | | | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Melike Bakır
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
| | - Eric J. B. von Wettberg
- Plant and Soil Science and Gund Institute for the Environment, The University of Vermont, Burlington, VT, United States
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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11
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High-density genetic map and genome-wide association studies of aesthetic traits in Phalaenopsis orchids. Sci Rep 2022; 12:3346. [PMID: 35228611 PMCID: PMC8885740 DOI: 10.1038/s41598-022-07318-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 02/11/2022] [Indexed: 11/26/2022] Open
Abstract
Phalaenopsis spp. represent the most popular orchids worldwide. Both P. equestris and P. aphrodite are the two important breeding parents with the whole genome sequence available. However, marker–trait association is rarely used for floral traits in Phalaenopsis breeding. Here, we analyzed markers associated with aesthetic traits of Phalaenopsis orchids by using genome-wide association study (GWAS) with the F1 population P. Intermedia of 117 progenies derived from the cross between P. aphrodite and P. equestris. A total of 113,517 single nucleotide polymorphisms (SNPs) were identified in P. Intermedia by using genotyping-by-sequencing with the combination of two different restriction enzyme pairs, Hinp1 I/Hae III and Apek I/Hae III. The size-related traits from flowers were negatively related to the color-related traits. The 1191 SNPs from Hinp1 I/ Hae III and 23 simple sequence repeats were used to establish a high-density genetic map of 19 homolog groups for P. equestris. In addition, 10 quantitative trait loci were highly associated with four color-related traits on chromosomes 2, 5 and 9. According to the sequence within the linkage disequilibrium regions, 35 candidate genes were identified and related to anthocyanin biosynthesis. In conclusion, we performed marker-assisted gene identification of aesthetic traits with GWAS in Phalaenopsis orchids.
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12
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Chepsergon J, Motaung TE, Moleleki LN. "Core" RxLR effectors in phytopathogenic oomycetes: A promising way to breeding for durable resistance in plants? Virulence 2021; 12:1921-1935. [PMID: 34304703 PMCID: PMC8516161 DOI: 10.1080/21505594.2021.1948277] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/11/2021] [Accepted: 06/18/2021] [Indexed: 12/30/2022] Open
Abstract
Phytopathogenic oomycetes are known to successfully infect their hosts due to their ability to secrete effector proteins. Of interest to many researchers are effectors with the N-terminal RxLR motif (Arginine-any amino acid-Leucine-Arginine). Owing to advances in genome sequencing, we can now comprehend the high level of diversity among oomycete effectors, and similarly, their conservation within and among species referred to here as "core" RxLR effectors (CREs). Currently, there is a considerable number of CREs that have been identified in oomycetes. Functional characterization of these CREs propose their virulence role with the potential of targeting central cellular processes that are conserved across diverse plant species. We reason that effectors that are highly conserved and recognized by the host, could be harnessed in engineering plants for durable as well as broad-spectrum resistance.
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Affiliation(s)
- Jane Chepsergon
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Thabiso E. Motaung
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
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13
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Zou K, Kim KS, Kim K, Kang D, Park YH, Sun H, Ha BK, Ha J, Jun TH. Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut ( Arachis hypogaea L.). Genes (Basel) 2020; 12:E2. [PMID: 33375051 PMCID: PMC7822046 DOI: 10.3390/genes12010002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/09/2020] [Accepted: 12/17/2020] [Indexed: 12/12/2022] Open
Abstract
Peanut (Arachis hypogaea L.) is one of the important oil crops of the world. In this study, we aimed to evaluate the genetic diversity of 384 peanut germplasms including 100 Korean germplasms and 284 core collections from the United States Department of Agriculture (USDA) using an Axiom_Arachis array with 58K single-nucleotide polymorphisms (SNPs). We evaluated the evolutionary relationships among 384 peanut germplasms using a genome-wide association study (GWAS) of seed aspect ratio data processed by ImageJ software. In total, 14,030 filtered polymorphic SNPs were identified from the peanut 58K SNP array. We identified five SNPs with significant associations to seed aspect ratio on chromosomes Aradu.A09, Aradu.A10, Araip.B08, and Araip.B09. AX-177640219 on chromosome Araip.B08 was the most significantly associated marker in GAPIT and Regularization method. Phosphoenolpyruvate carboxylase (PEPC) was found among the eleven genes within a linkage disequilibrium (LD) of the significant SNPs on Araip.B08 and could have a strong causal effect in determining seed aspect ratio. The results of the present study provide information and methods that are useful for further genetic and genomic studies as well as molecular breeding programs in peanuts.
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Affiliation(s)
- Kunyan Zou
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea; (K.Z.); (D.K.); (Y.-H.P.)
| | | | - Kipoong Kim
- Department of Statistics, Pusan National University, Busan 46241, Korea; (K.K.); (H.S.)
| | - Dongwoo Kang
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea; (K.Z.); (D.K.); (Y.-H.P.)
| | - Yu-Hyeon Park
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea; (K.Z.); (D.K.); (Y.-H.P.)
| | - Hokeun Sun
- Department of Statistics, Pusan National University, Busan 46241, Korea; (K.K.); (H.S.)
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea;
| | - Jungmin Ha
- Department of Plant Science, Gangneung-Wonju National University, Gangneung 25457, Korea;
| | - Tae-Hwan Jun
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea; (K.Z.); (D.K.); (Y.-H.P.)
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Korea
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14
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Plewiński P, Ćwiek-Kupczyńska H, Rudy E, Bielski W, Rychel-Bielska S, Stawiński S, Barzyk P, Krajewski P, Naganowska B, Wolko B, Książkiewicz M. Innovative transcriptome-based genotyping highlights environmentally responsive genes for phenology, growth and yield in a non-model grain legume. PLANT, CELL & ENVIRONMENT 2020; 43:2680-2698. [PMID: 32885839 DOI: 10.1111/pce.13880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/21/2020] [Accepted: 08/22/2020] [Indexed: 06/11/2023]
Abstract
The narrow-leafed lupin, Lupinus angustifolius L., is a grain legume crop, cultivated both as a green manure and as a source of protein for animal feed and human food production. During its domestication process, numerous agronomic traits were improved, however, only two trait-related genes were identified hitherto, both by linkage mapping. Genome-wide association studies (GWAS), exploiting genomic sequencing, did not select any novel candidate gene. In the present study, an innovative method of 3'-end reduced representation transcriptomic profiling, a massive analysis of cDNA ends, has been used for genotyping of 126 L. angustifolius lines surveyed by field phenotyping. Significant genotype × environment interactions were identified for all phenology and yield traits analysed. Principal component analysis of population structure evidenced European domestication bottlenecks, visualized by clustering of breeding materials and cultivars. GWAS provided contribution towards deciphering vernalization pathway in legumes, and, apart from highlighting known domestication loci (Ku/Julius and mol), designated novel candidate genes for L. angustifolius traits. Early phenology was associated with genes from vernalization, cold-responsiveness and phosphatidylinositol signalling pathways whereas high yield with genes controlling photosynthesis performance and abiotic stress (drought or heat) tolerance. PCR-based toolbox was developed and validated to enable tracking desired alleles in marker-assisted selection. Narrow-leafed lupin was genotyped with an innovative method of transcriptome profiling and phenotyped for phenology, growth and yield traits in field. Early phenology was found associated with genes from cold-response, vernalization and phosphatidylinositol signalling pathways, whereas high yield with genes running photosystem II and drought or heat stress response. Key loci were supplied with PCR-based toolbox for marker-assisted selection.
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Affiliation(s)
- Piotr Plewiński
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Hanna Ćwiek-Kupczyńska
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Elżbieta Rudy
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Wojciech Bielski
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Sandra Rychel-Bielska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Stanisław Stawiński
- Department in Przebędowo, Plant Breeding Smolice Ltd., Murowana Goślina, Poland
| | - Paweł Barzyk
- Department in Wiatrowo, Poznań Plant Breeding Ltd., Wiatrowo, Poland
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Bogdan Wolko
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Michał Książkiewicz
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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15
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Kumar J, Sen Gupta D. Prospects of next generation sequencing in lentil breeding. Mol Biol Rep 2020; 47:9043-9053. [PMID: 33037962 DOI: 10.1007/s11033-020-05891-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 10/03/2020] [Indexed: 11/28/2022]
Abstract
Lentil is an important food legume crop that has large and complex genome. During past years, considerable attention has been given on the use of next generation sequencing for enriching the genomic resources including identification of SSR and SNP markers, development of unigenes, transcripts, and identification of candidate genes for biotic and abiotic stresses, analysis of genetic diversity and identification of genes/ QTLs for agronomically important traits. However, in other crops including pulses, next generation sequencing has revolutionized the genomic research and helped in genomic assisted breeding rapidly and cost effectively. The present review discuss current status and future prospects of the use NGS based breeding in lentil.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India.
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India
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16
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Rychel-Bielska S, Nazzicari N, Plewiński P, Bielski W, Annicchiarico P, Książkiewicz M. Development of PCR-based markers and whole-genome selection model for anthracnose resistance in white lupin (Lupinus albus L.). J Appl Genet 2020; 61:531-545. [PMID: 32968972 PMCID: PMC7652745 DOI: 10.1007/s13353-020-00585-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022]
Abstract
White lupin (Lupinus albus L.) is a high-protein grain legume crop, grown since ancient Greece and Rome. Despite long domestication history, its cultivation remains limited, partly because of susceptibility to anthracnose. Only some late-flowering, bitter, low-yielding landraces from Ethiopian mountains displayed resistance to this devastating disease. The resistance is controlled by various genes, thereby complicating the breeding efforts. The objective of this study was developing tools for molecular tracking of Ethiopian resistance genes based on genotyping-by-sequencing (GBS) data, envisaging linkage mapping and genomic selection approaches. Twenty GBS markers from two major quantitative trait loci (QTLs), antr04_1/antr05_1 and antr04_2/antr05_2, were converted to PCR-based markers using assigned transcriptome sequences. Newly developed markers improved mapping resolution around both anthracnose resistance loci, providing more precise QTL estimation. PCR-based screening of diversified domesticated and primitive germplasm revealed the high specificity of two markers for the antr04_1/antr05_1 locus (TP222136 and TP47110) and one for the antr04_2/antr05_2 locus (TP338761), highlighted by simple matching coefficients of 0.96 and 0.89, respectively. Moreover, a genomic selection approach based on GBS data of a recombinant inbred line mapping population was assessed, providing an average predictive ability of 0.56. These tools can be used for preselection of candidate white lupin germplasm for anthracnose resistance assays.
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Affiliation(s)
- Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 24A, 50-363, Wrocław, Poland.,Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Nelson Nazzicari
- CREA-FLC, Council for Agricultural Research and Economics, Research Centre for Fodder Crops and Dairy Production, Viale Piacenza 29, 26900, Lodi, Italy
| | - Piotr Plewiński
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Wojciech Bielski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Paolo Annicchiarico
- CREA-FLC, Council for Agricultural Research and Economics, Research Centre for Fodder Crops and Dairy Production, Viale Piacenza 29, 26900, Lodi, Italy
| | - Michał Książkiewicz
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
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17
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Babu P, Baranwal DK, Harikrishna, Pal D, Bharti H, Joshi P, Thiyagarajan B, Gaikwad KB, Bhardwaj SC, Singh GP, Singh A. Application of Genomics Tools in Wheat Breeding to Attain Durable Rust Resistance. FRONTIERS IN PLANT SCIENCE 2020; 11:567147. [PMID: 33013989 PMCID: PMC7516254 DOI: 10.3389/fpls.2020.567147] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/12/2020] [Indexed: 11/13/2023]
Abstract
Wheat is an important source of dietary protein and calories for the majority of the world's population. It is one of the largest grown cereal in the world occupying over 215 M ha. Wheat production globally is challenged by biotic stresses such as pests and diseases. Of the 50 diseases of wheat that are of economic importance, the three rust diseases are the most ubiquitous causing significant yield losses in the majority of wheat production environments. Under severe epidemics they can lead to food insecurity threats amid the continuous evolution of new races of the pathogens, shifts in population dynamics and their virulence patterns, thereby rendering several effective resistance genes deployed in wheat breeding programs vulnerable. This emphasizes the need to identify, characterize, and deploy effective rust-resistant genes from diverse sources into pre-breeding lines and future wheat varieties. The use of genetic resistance has been marked as eco-friendly and to curb the further evolution of rust pathogens. Deployment of multiple rust resistance genes including major and minor genes in wheat lines could enhance the durability of resistance thereby reducing pathogen evolution. Advances in next-generation sequencing (NGS) platforms and associated bioinformatics tools have revolutionized wheat genomics. The sequence alignment of the wheat genome is the most important landmark which will enable genomics to identify marker-trait associations, candidate genes and enhanced breeding values in genomic selection (GS) studies. High throughput genotyping platforms have demonstrated their role in the estimation of genetic diversity, construction of the high-density genetic maps, dissecting polygenic traits, and better understanding their interactions through GWAS (genome-wide association studies) and QTL mapping, and isolation of R genes. Application of breeder's friendly KASP assays in the wheat breeding program has expedited the identification and pyramiding of rust resistance alleles/genes in elite lines. The present review covers the evolutionary trends of the rust pathogen and contemporary wheat varieties, and how these research strategies galvanized to control the wheat killer genus Puccinia. It will also highlight the outcome and research impact of cost-effective NGS technologies and cloning of rust resistance genes amid the public availability of common and tetraploid wheat reference genomes.
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Affiliation(s)
- Prashanth Babu
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | - Harikrishna
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Dharam Pal
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Hemlata Bharti
- Directorate of Medicinal and Aromatic Plants Research (ICAR), Anand, India
| | - Priyanka Joshi
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | | | | | | | | | - Anupam Singh
- DCM SHRIRAM-Bioseed Research India, ICRISAT, Hyderabad, India
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18
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Olivieri F, Calafiore R, Francesca S, Schettini C, Chiaiese P, Rigano MM, Barone A. High-Throughput Genotyping of Resilient Tomato Landraces to Detect Candidate Genes Involved in the Response to High Temperatures. Genes (Basel) 2020; 11:genes11060626. [PMID: 32517343 PMCID: PMC7349060 DOI: 10.3390/genes11060626] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 12/04/2022] Open
Abstract
The selection of tolerant varieties is a powerful strategy to ensure highly stable yield under elevated temperatures. In this paper, we report the phenotypic and genotypic characterization of 10 tomato landraces to identify the best performing under high temperatures. The phenotyping of five yield-related traits allowed us to select one genotype that exhibits highly stable yield performances in different environmental conditions. Moreover, a Genotyping-by-Sequencing approach allowed us to explore the genetic variability of the tested genotypes. The high and stable yielding landrace E42 was the most polymorphic one, with ~49% and ~47% private SNPs and InDels, respectively. The effect of 26,113 mutations on proteins’ structure was investigated and it was discovered that 37 had a high impact on the structure of 34 proteins of which some are putatively involved in responses to high temperatures. Additionally, 129 polymorphic sequences aligned against tomato wild species genomes revealed the presence in the genotype E42 of several introgressed regions deriving from S. pimpinellifolium. The position on the tomato map of genes affected by moderate and high impact mutations was also compared with that of known markers/QTLs (Quantitative Trait Loci) associated with reproductive and yield-related traits. The candidate genes/QTLs regulating heat tolerance in the selected landrace E42 could be further investigated to better understand the genetic mechanisms controlling traits for high and stable yield trait under high temperatures.
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Affiliation(s)
- Fabrizio Olivieri
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Napoli, Italy; (F.O.); (R.C.); (S.F.); (P.C.); (M.M.R.)
| | - Roberta Calafiore
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Napoli, Italy; (F.O.); (R.C.); (S.F.); (P.C.); (M.M.R.)
| | - Silvana Francesca
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Napoli, Italy; (F.O.); (R.C.); (S.F.); (P.C.); (M.M.R.)
| | | | - Pasquale Chiaiese
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Napoli, Italy; (F.O.); (R.C.); (S.F.); (P.C.); (M.M.R.)
| | - Maria Manuela Rigano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Napoli, Italy; (F.O.); (R.C.); (S.F.); (P.C.); (M.M.R.)
| | - Amalia Barone
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Napoli, Italy; (F.O.); (R.C.); (S.F.); (P.C.); (M.M.R.)
- Correspondence: ; Tel.: +39-0812539491
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19
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Książkiewicz M, Yang H. Molecular Marker Resources Supporting the Australian Lupin Breeding Program. COMPENDIUM OF PLANT GENOMES 2020. [DOI: 10.1007/978-3-030-21270-4_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Zhao Q, Wu J, Cai G, Yang Q, Shahid M, Fan C, Zhang C, Zhou Y. A novel quantitative trait locus on chromosome A9 controlling oleic acid content in Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2313-2324. [PMID: 31037811 PMCID: PMC6835171 DOI: 10.1111/pbi.13142] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 05/09/2023]
Abstract
One of the most important goals in the breeding of oilseed crops, including Brassica napus, is to improve the quality of edible vegetable oil, which is mainly determined by the seed fatty acid composition, particularly the C18:1 content. Previous studies have indicated that the C18:1 content is a polygenic trait, and no stable quantitative trait loci (QTLs) except for FAD2 have been reported. By performing a GWAS using 375 low erucic acid B. napus accessions genotyped with the Brassica 60K SNP array and constructing a high-density SNP-based genetic map of a 150 DH population, we identified a novel QTL on the A9 chromosome. The novel locus could explain 11.25%, 5.72% and 6.29% of phenotypic variation during three consecutive seasons and increased the C18:1 content by approximately 3%-5%. By fine mapping and gene expression analysis, we found three potential candidate genes and verified the fatty acids in a homologous gene mutant of Arabidopsis. A metal ion-binding protein was found to be the most likely candidate gene in the region. Thus, the C18:1 content can be further increased to about 80% with this novel locus together with FAD2 mutant allele without compromise of agronomic performance. A closely linked marker, BnA129, for this novel QTL (OLEA9) was developed so that we can effectively identify materials with high C18:1 content at an early growth stage by marker-assisted selection. Our results may also provide new insight for understanding the complex genetic mechanism of fatty acid metabolism.
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Affiliation(s)
- Qing Zhao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Jian Wu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Present address:
Jiangsu Provincial Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhou225009JiangsuChina
| | - Guangqin Cai
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Qingyong Yang
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanHubeiChina
| | - Muhammad Shahid
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
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21
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Review: Molecular techniques to assess genetic variation within and between Panax ginseng and Panax quinquefolius. Fitoterapia 2019; 138:104343. [PMID: 31472181 DOI: 10.1016/j.fitote.2019.104343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/19/2019] [Accepted: 08/25/2019] [Indexed: 11/23/2022]
Abstract
A variety of methods have been used to examine genetic differences in P. ginseng and P. quinquefolius. They have shown genetic differences within populations of P. ginseng (within and between elite cultivars, landraces and wild accessions), within populations of P. quinquefolius (within and between wild and cultivated accessions) and between P. ginseng and P. quinquefolius as well as other Panax species. Some examples of their applications have been to show that some elite cultivars are not uniform, there are possible founder effects in certain populations, there has been the spread of cultivated types into wild populations, relative diversity differs between different populations and identification of the source and purity of commercial samples. More work in the use of molecular markers for ginseng are needed, however, particularly the use of Next Generation Sequencing. Potential applications are the use of sequence analysis for genetic selection, breeding to develop new cultivars and providing traceability from field to consumer. Research on molecular markers in ginseng has lagged compared to other crops probably because of less of an emphasis on breeding for cultivar development and relatively small areas of production. The many potential benefits for ginseng production have yet to be realized.
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Genome-wide RAD sequencing to identify a sex-specific marker in Chinese giant salamander Andrias davidianus. BMC Genomics 2019; 20:415. [PMID: 31122206 PMCID: PMC6533744 DOI: 10.1186/s12864-019-5771-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 05/03/2019] [Indexed: 11/15/2022] Open
Abstract
Background Chinese giant salamander Andrias davidianus is an endangered species. The success of artificial breeding provides a useful way to protect this species. However, the method to identify the sex and mechanism of sex determination were unclear which hinder the improvement of the artificial breeding. Detection of a sex specific marker provides an effective approach to identify genetic sex and investigate the sex determination mechanism. Results We used restriction-site-associated DNA (RAD) sequencing to isolate a sex-specific genetic marker in A. davidianus to expand knowledge of the sex determination mechanism. Four male and four female specimens were subjected to RAD sequencing, which generated 934,072,989 reads containing approximately 134.4 Gb of sequences. The first round of comparison of the assembled sequence against the opposite sex raw reads revealed 19,097 female and 17,994 male unmatched sequences. Subsequently, 19,097 female sequences were subjected to a BLAST search against male genomic data, which revealed 308 sequences unmapped to the male genome. One hundred of these were randomly selected and validated by PCR in five male and five female specimens, and four putative sex-specific sequences were produced. Further validation was performed by PCR in another 24 females and 24 males, and all female individuals exhibited the expected specific bands, while the males did not. To apply the sex-specific marker, three specimens reversed from genetic female to physiological male were found in a group exposed to elevated temperature, and 13 individuals reversed from genetic male to physiological female were obtained in a 17β-estradiol exposed group. Conclusion This is the first report of a sex-specific marker in A. davidianus and may have potential for elucidation of its sex determination mechanism and, hence, its conservation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5771-5) contains supplementary material, which is available to authorized users.
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Abraham EM, Ganopoulos I, Madesis P, Mavromatis A, Mylona P, Nianiou-Obeidat I, Parissi Z, Polidoros A, Tani E, Vlachostergios D. The Use of Lupin as a Source of Protein in Animal Feeding: Genomic Tools and Breeding Approaches. Int J Mol Sci 2019; 20:ijms20040851. [PMID: 30781397 PMCID: PMC6413129 DOI: 10.3390/ijms20040851] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/08/2019] [Accepted: 02/10/2019] [Indexed: 12/05/2022] Open
Abstract
Livestock production in the European Union EU is highly dependent on imported soybean, exposing the livestock farming system to risks related to the global trade of soybean. Lupin species could be a realistic sustainable alternative source of protein for animal feeding. Lupinus is a very diverse genus with many species. However, only four of them—namely, L. albus, L. angustifolius, L. luteus and L. mutabilis—are cultivated. Their use in livestock farming systems has many advantages in relation to economic and environmental impact. Generally, lupin grains are characterized by high protein content, while their oil content is relatively low but of high quality. On the other hand, the presence of quinolizidine alkaloids and their specific carbohydrate composition are the main antinutritional factors that prevent their use in animal feeding. This research is mainly related to L. albus and to L. angustifolius, and to a lesser extent, to L. lauteus and L. mutabilis. The breeding efforts are mostly focused on yield stabilization, resistance to biotic and abiotic stresses, biochemical structure associated with seed quality and late maturing. Progress is made in improving lupin with respect to the seed quality, as well as the tolerance to biotic and abiotic stress. It has to be noted that modern cultivars, mostly of L. albus and L. angustifolius, contain low levels of alkaloids. However, for future breeding efforts, the implementation of marker-assisted selection and the available genomic tools is of great importance.
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Affiliation(s)
- Eleni M Abraham
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, Thermi, 57001 Thessaloniki, Greece.
| | | | - Athanasios Mavromatis
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Photini Mylona
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, Thermi, 57001 Thessaloniki, Greece.
| | - Irini Nianiou-Obeidat
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Zoi Parissi
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Alexios Polidoros
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Eleni Tani
- Department of Crop Science, Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
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Wang H, Zaman QU, Huang W, Mei D, Liu J, Wang W, Ding B, Hao M, Fu L, Cheng H, Hu Q. QTL and Candidate Gene Identification for Silique Length Based on High-Dense Genetic Map in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2019; 10:1579. [PMID: 31850044 PMCID: PMC6895753 DOI: 10.3389/fpls.2019.01579] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/12/2019] [Indexed: 05/13/2023]
Abstract
Silique length (SL) is an important yield trait and positively correlates with seeds per silique and seed weight. In the present study, two double haploid (DH) populations, established from crosses Zhongshuang11 × R11 (ZR) and R1 × R2 (RR), containing 280 and 95 DH lines, respectively, were used to map quantitative trait loci (QTL) for SL. A high-dense genetic map from ZR population was constructed comprising 14,658 bins on 19 linkage groups, with map length of 2,198.85 cM and an average marker distance of 0.15 cM. Genetic linkage map from RR population was constructed by using 2,046 mapped markers anchored to 19 chromosomes with 2,217-cM map length and an average marker distance of 1.08 cM. Major QTL qSL_ZR_A09 and qSL_RR_A09b on A09 were identified from ZR and RR populations, respectively. Both QTL could be stably detected in four environments. QTL qSL_RR_A09b and qSL_ZR_A09 were located on 68.5-70.8 cM and 91.33-91.94 cM interval with R2 values of 14.99-39.07% and 15.00-20.36% in RR and ZR populations, respectively. Based on the physical positions of single nucleotide polymorphism (SNP) markers flanking qSL_ZR_A09 and gene annotation in Arabidopsis, 26 genes were identified with SNP/Indel variation between parents and two genes (BnaA09g41180D and BnaA09g41380D) were selected as the candidate genes. Expression analysis further revealed BnaA09g41180D, encoding homologs of Arabidopsis fasciclin-like arabinogalactan proteins (FLA3), as the most promising candidate gene for qSL_ZR_A09. The QTL identification and candidate gene analysis will provide new insight into the genomic regions controlling SL in Brassica napus as well as candidate genes underlying the QTL.
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Affiliation(s)
- Hui Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qamar U. Zaman
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
- Graduate School of the Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenhui Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Desheng Mei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jia Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Wenxiang Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Bingli Ding
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Mengyu Hao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Li Fu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Hongtao Cheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
- *Correspondence: Hongtao Cheng ; Qiong Hu
| | - Qiong Hu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
- *Correspondence: Hongtao Cheng ; Qiong Hu
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Carrasco B, González M, Gebauer M, García-González R, Maldonado J, Silva H. Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling. PLoS One 2018; 13:e0208032. [PMID: 30507961 PMCID: PMC6277071 DOI: 10.1371/journal.pone.0208032] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/09/2018] [Indexed: 11/19/2022] Open
Abstract
This study reports the construction of high density linkage maps of Japanese plum (Prunus salicina Lindl.) using single nucleotide polymorphism markers (SNPs), obtained with a GBS strategy. The mapping population (An x Au) was obtained by crossing cv. "Angeleno" (An) as maternal line and cv. "Aurora" (Au) as the pollen donor. A total of 49,826 SNPs were identified using the peach genome V2.1 as a reference. Then a stringent filtering was carried out, which revealed 1,441 high quality SNPs in 137 An x Au offspring, which were mapped in eight linkage groups. Finally, the consensus map was built using 732 SNPs which spanned 617 cM with an average of 0.96 cM between adjacent markers. The majority of the SNPs were distributed in the intragenic region in all the linkage groups. Considering all linkage groups together, 85.6% of the SNPs were located in intragenic regions and only 14.4% were located in intergenic regions. The genetic linkage analysis was able to co-localize two to three SNPs over 37 putative orthologous genes in eight linkage groups in the Japanese plum map. These results indicate a high level of synteny and collinearity between Japanese plum and peach genomes.
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Affiliation(s)
- Basilio Carrasco
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Ciencias Vegetales, Macul, Santiago, Chile
| | - Máximo González
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Ciencias Vegetales, Macul, Santiago, Chile
| | - Marlene Gebauer
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Ciencias Vegetales, Macul, Santiago, Chile
| | - Rolando García-González
- Sociedad BioTECNOS Ltda, R&D Department Camino a Pangal Km 2 1/2, San Javier, Región del Maule, Chile
- Facultad de Ciencias Agrarias y Forestales, Centro de Biotecnología de los Recursos Naturales (CENBio), Universidad Católica del Maule, Talca, Chile
| | - Jonathan Maldonado
- Universidad de Chile, Facultad de Ciencias Agronómicas, Departamento de Producción Agrícola, Laboratorio de Genómica Funcional & Bioinformática, La Pintana, Santiago, Chile
| | - Herman Silva
- Universidad de Chile, Facultad de Ciencias Agronómicas, Departamento de Producción Agrícola, Laboratorio de Genómica Funcional & Bioinformática, La Pintana, Santiago, Chile
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Ridzuan R, Rafii MY, Ismail SI, Mohammad Yusoff M, Miah G, Usman M. Breeding for Anthracnose Disease Resistance in Chili: Progress and Prospects. Int J Mol Sci 2018; 19:E3122. [PMID: 30314374 PMCID: PMC6213496 DOI: 10.3390/ijms19103122] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/17/2018] [Accepted: 08/18/2018] [Indexed: 11/16/2022] Open
Abstract
Chili anthracnose is one of the most devastating fungal diseases affecting the quality and yield production of chili. The aim of this review is to summarize the current knowledge concerning the chili anthracnose disease, as well as to explore the use of marker-assisted breeding programs aimed at improving anthracnose disease resistance in this species. This disease is caused by the Colletotrichum species complex, and there have been ongoing screening methods of chili pepper genotypes with resistance to anthracnose in the field, as well as in laboratories. Conventional breeding involves phenotypic selection in the field, and it is more time-consuming compared to molecular breeding. The use of marker-assisted selection (MAS) on the basis of inheritance, the segregation ratio of resistance to susceptibility, and the gene-controlling resistance may contribute to the development of an improved chili variety and speed up the selection process, while also reducing genetic drag in the segregating population. More importantly, by using molecular markers, the linkage groups are determined dominantly and co-dominantly, meaning that the implementation of a reliable method to produce resistant varieties is crucial in future breeding programs. This updated information will offer a supportive direction for chili breeders to develop an anthracnose-resistant chili variety.
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Affiliation(s)
- Raihana Ridzuan
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Mohd Y Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Martini Mohammad Yusoff
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Gous Miah
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Magaji Usman
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
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Li J, Guo H, Wang Y, Zong J, Chen J, Li D, Li L, Wang J, Liu J. High-throughput SSR marker development and its application in a centipedegrass (Eremochloa ophiuroides (Munro) Hack.) genetic diversity analysis. PLoS One 2018; 13:e0202605. [PMID: 30133524 PMCID: PMC6105027 DOI: 10.1371/journal.pone.0202605] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/05/2018] [Indexed: 11/18/2022] Open
Abstract
Centipedegrass (Eremochloa ophiuroides (Munro) Hack.) is a perennial, warm-season C4 grass species that shows great potential for use as a low-maintenance turfgrass species in tropical and subtropical regions. However, limited genetic and genomic information is available for this species, which has impeded systematic studies on the enhancement of its turf quality and resistance against biotic and abiotic stress. In this study, Illumina HiSeq high-throughput sequencing technology was performed to generate centipedegrass transcriptome sequences. A total of 352,513 assembled sequences were used to search for simple sequence repeat (SSR) loci, and 64,470 SSR loci were detected in 47,638 SSR containing sequences. The tri-nucleotides were the most frequent repeat motif, followed by di-nucleotides, tetra-nucleotides hexnucleotides, and pentanucleotides. A total of 48,061 primer pairs were successfully designed in the flanking sequences of the SSRs, and 100 sets of primers were randomly selected for the initial validation in four centipedegrass accessions. In total, 56 (56.0%) of the 100 primer pairs tested successfully amplified alleles from all four centipedegrass accessions, while 50 were identified as polymorphic markers and were then used to assess the level of genetic diversity among 43 centipedegrass core collections. The genetic diversity analysis exhibited that the number of alleles (Na) per locus ranged from 3 to 13, and the observed heterozygosity (Ho) ranged from 0.17 to 0.83. The polymorphism information content (PIC) value of the markers ranged from 0.15 to 0.78, and the genetic distances (coefficient Nei72) between the accessions varied from 0.07 to 0.48. The UPGMA-based dendrogram clustered all 43 core collections into two main groups and six subgroups, which further validated the effectiveness of these newly developed SSR markers. Hence, these newly developed SSR markers will be valuable and potentially useful for future genetic and genomic studies of E. ophiuroides.
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Affiliation(s)
- Jianjian Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Hailin Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Yi Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Junqin Zong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Jingbo Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Dandan Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Ling Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Jingjing Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
- * E-mail:
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Yang S, Chen S, Zhang K, Li L, Yin Y, Gill RA, Yan G, Meng J, Cowling WA, Zhou W. A High-Density Genetic Map of an Allohexaploid Brassica Doubled Haploid Population Reveals Quantitative Trait Loci for Pollen Viability and Fertility. FRONTIERS IN PLANT SCIENCE 2018; 9:1161. [PMID: 30210508 PMCID: PMC6123574 DOI: 10.3389/fpls.2018.01161] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/23/2018] [Indexed: 05/02/2023]
Abstract
A doubled haploid (DH) mapping population was obtained from microspore culture of an allohexaploid F1 from the cross between two recently-synthesized allohexaploid Brassica lines. We used single nucleotide polymorphism (SNP) genetic variation based on restriction-site associated DNA (RAD) sequencing to construct a high density genetic linkage map of the population. RAD libraries were constructed from the genomic DNA of both parents and 146 DH progenies. A total of 2.87 G reads with an average sequencing depth of 2.59 × were obtained in the parents and of 1.41 × in the progeny. A total of 290,422 SNPs were identified from clustering of RAD reads, from which we developed 7,950 high quality SNP markers that segregated normally (1:1) in the population. The linkage map contained all 27 chromosomes from the parental A, B and C genomes with a total genetic distance of 5725.19 cM and an average of 0.75 cM between adjacent markers. Genetic distance on non-integrated linkage groups was 1534.23 cM, or 21% of total genetic distance. Out of 146 DH progenies, 91 had a complete set of 27 chromosomes as expected of a hexaploid species, and 21 out of 27 chromosomes showed high collinearity between the physical and linkage maps. The loss of chromosome(s) or chromosome segment(s) in the DH population was associated with a reduction in pollen viability. Twenty-five additive QTL were associated with pollen viability and fertility-related traits (seed number, seed yield, pod length, plant height, 1000-seed weight). In addition, 44 intra-genomic and 18 inter-genomic epistatic QTL pairs were detected for 4 phenotypic traits. This provides confidence that the DH population may be selected for improved pollen viability and fertility in a future allohexaploid Brassica species.
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Affiliation(s)
- Su Yang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Sheng Chen
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Perth, WA, Australia
| | - Kangni Zhang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Lan Li
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Yuling Yin
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Rafaqat A. Gill
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Guijun Yan
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Perth, WA, Australia
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wallace A. Cowling
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Perth, WA, Australia
- School of Biological Sciences, Faculty of Science, The University of Western Australia, Perth, WA, Australia
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
- *Correspondence: Weijun Zhou
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Zhou G, Jian J, Wang P, Li C, Tao Y, Li X, Renshaw D, Clements J, Sweetingham M, Yang H. Construction of an ultra-high density consensus genetic map, and enhancement of the physical map from genome sequencing in Lupinus angustifolius. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:209-223. [PMID: 29051970 DOI: 10.1007/s00122-017-2997-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/01/2017] [Indexed: 05/04/2023]
Abstract
An ultra-high density genetic map containing 34,574 sequence-defined markers was developed in Lupinus angustifolius. Markers closely linked to nine genes of agronomic traits were identified. A physical map was improved to cover 560.5 Mb genome sequence. Lupin (Lupinus angustifolius L.) is a recently domesticated legume grain crop. In this study, we applied the restriction-site associated DNA sequencing (RADseq) method to genotype an F9 recombinant inbred line population derived from a wild type × domesticated cultivar (W × D) cross. A high density linkage map was developed based on the W × D population. By integrating sequence-defined DNA markers reported in previous mapping studies, we established an ultra-high density consensus genetic map, which contains 34,574 markers consisting of 3508 loci covering 2399 cM on 20 linkage groups. The largest gap in the entire consensus map was 4.73 cM. The high density W × D map and the consensus map were used to develop an improved physical map, which covered 560.5 Mb of genome sequence data. The ultra-high density consensus linkage map, the improved physical map and the markers linked to genes of breeding interest reported in this study provide a common tool for genome sequence assembly, structural genomics, comparative genomics, functional genomics, QTL mapping, and molecular plant breeding in lupin.
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Affiliation(s)
- Gaofeng Zhou
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia
| | - Jianbo Jian
- Beijing Genome Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Penghao Wang
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia
| | - Chengdao Li
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia
| | - Ye Tao
- BIOZERON Biotechnology Co., Ltd.-Shanghai, Xingxian Road, 1180-7, Shanghai, 210880, China
| | - Xuan Li
- Beijing Genome Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Daniel Renshaw
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Jonathan Clements
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Mark Sweetingham
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Huaan Yang
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia.
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Zaccaron M, Sharma S, Bluhm BH. MoNSTR-seq, a restriction site-associated DNA sequencing technique to characterize Agrobacterium-mediated transfer-DNA insertions in Phomopsis longicolla. Lett Appl Microbiol 2018; 66:19-24. [PMID: 29108115 DOI: 10.1111/lam.12817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 10/14/2017] [Accepted: 10/24/2017] [Indexed: 11/26/2022]
Abstract
Phomopsis longicolla (Hobbs) causes Phomopsis seed decay and stem lesions in soybean (Glycine max). In this study, a novel, high-throughput adaptation of RAD-seq termed MoNSTR-seq (Mutation analysis via Next-generation DNA Sequencing of T-DNA Regions) was developed to determine the genomic location of T-DNA insertions in P. longicolla mutants. Insertional mutants were created via Agrobacterium tumefaciens-mediated transformation, and one mutant, strain PL343, was further investigated due to impaired stem lesion formation. Mutation analysis via Next-generation DNA Sequencing of T-DNA Regions, in which DNA libraries are created with two distinct restriction enzymes and customized adapters to simultaneously enrich both T-DNA insertion borders, was developed to characterize the genomic lesion in strain PL343. MoNSTR-seq successfully identified a T-DNA insertion in the predicted promoter region of a gene encoding a cellobiose dehydrogenase (CDH1), and the position of the T-DNA insertion in strain PL343 was confirmed by Sanger sequencing. Thus, MoNSTR-seq represents an effective tool for molecular genetics in P. longicolla, and is readily adaptable for use in diverse fungal species. SIGNIFICANCE AND IMPACT OF THE STUDY This study describes MoNSTR-seq (Mutation analysis via Next-generation DNA Sequencing of T-DNA Regions), an adaptation of restriction site-associated DNA sequencing (RAD-seq) to identify the position of transfer-DNA (T-DNA) insertions in the genome of Phomopsis longicolla, an important pathogen of soybean. The technique enables high-throughput characterization of mutants generated via Agrobacterium tumefaciens-mediated transformation (ATMT), thus accelerating gene discovery via forward genetics. This technique represents a significant advancement over existing approaches to characterize T-DNA insertions in fungal genomes. With minor modifications, this technique could be easily adapted to taxonomically diverse fungal pathogens and additional mutagenesis cassettes.
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Affiliation(s)
- M Zaccaron
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, USA
| | - S Sharma
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, USA
| | - B H Bluhm
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, USA
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Tsai WC, Dievart A, Hsu CC, Hsiao YY, Chiou SY, Huang H, Chen HH. Post genomics era for orchid research. BOTANICAL STUDIES 2017; 58:61. [PMID: 29234904 PMCID: PMC5727007 DOI: 10.1186/s40529-017-0213-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/01/2017] [Indexed: 05/05/2023]
Abstract
Among 300,000 species in angiosperms, Orchidaceae containing 30,000 species is one of the largest families. Almost every habitats on earth have orchid plants successfully colonized, and it indicates that orchids are among the plants with significant ecological and evolutionary importance. So far, four orchid genomes have been sequenced, including Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen. Here, we review the current progress and the direction of orchid research in the post genomics era. These include the orchid genome evolution, genome mapping (genome-wide association analysis, genetic map, physical map), comparative genomics (especially receptor-like kinase and terpene synthase), secondary metabolomics, and genome editing.
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Affiliation(s)
- Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Anne Dievart
- CIRAD, UMR AGAP, TA A 108/03, Avenue Agropolis, 34398 Montpellier, France
- Present Address: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Life Sciences Building, Room 3-117, Shanghai, 200240 People’s Republic of China
| | - Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Shang-Yi Chiou
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hsin Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hong-Hwa Chen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
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Molecular genetic diversity and population structure of Ethiopian white lupin landraces: Implications for breeding and conservation. PLoS One 2017; 12:e0188696. [PMID: 29190792 PMCID: PMC5708786 DOI: 10.1371/journal.pone.0188696] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 11/11/2017] [Indexed: 01/22/2023] Open
Abstract
White lupin is one of the four economically important species of the Lupinus genus and is an important grain legume in the Ethiopian farming system. However, there has been limited research effort to characterize the Ethiopian white lupin landraces. Fifteen polymorphic simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 212 Ethiopian white lupin (Lupinus albus) landraces and two genotypes from different species (Lupinus angustifolius and Lupinus mutabilis) were used as out-group. The SSR markers revealed 108 different alleles, 98 of them from 212 landraces and 10 from out-group genotypes, with an average of 6.5 alleles per locus. The average gene diversity was 0.31. Twenty eight landraces harbored one or more private alleles from the total of 28 private alleles identified in the 212 white lupin accessions. Seventy-seven rare alleles with a frequency of less than 5% were identified and accounted for 78.6% of the total alleles detected. Analysis of molecular variance (AMOVA) showed that 92% of allelic diversity was attributed to individual accessions within populations while only 8% was distributed among populations. At 70% similarity level, the UPGMA dendrogram resulted in the formation of 13 clusters comprised of 2 to 136 landraces, with the out-group genotypes and five landraces remaining distinct and ungrouped. Population differentiation and genetic distance were relatively high between Gondar and Ethiopian white lupin populations collected by Australians. A model-based population structure analysis divided the white lupin landraces into two populations. All Ethiopian white lupin landrace populations, except most of the landraces collected by Australians (77%) and about 44% from Awi, were grouped together with significant admixtures. The study also suggested that 34 accessions, as core collections, were sufficient to retain 100% of SSR diversity. These accessions (core G-34) represent 16% of the whole 212 Ethiopian white lupin accessions and populations from West Gojam, Awi and Australian collections contributed more accessions to the core collection.
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Iquebal MA, Jaiswal S, Mahato AK, Jayaswal PK, Angadi UB, Kumar N, Sharma N, Singh AK, Srivastav M, Prakash J, Singh SK, Khan K, Mishra RK, Rajan S, Bajpai A, Sandhya BS, Nischita P, Ravishankar KV, Dinesh MR, Rai A, Kumar D, Sharma TR, Singh NK. MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation. Sci Rep 2017; 7:14968. [PMID: 29097776 PMCID: PMC5668432 DOI: 10.1038/s41598-017-14998-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/20/2017] [Indexed: 01/20/2023] Open
Abstract
Mango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world’s first web-based genomic resources for genetic improvement and germplasm management of mango.
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Affiliation(s)
- M A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India
| | - Ajay Kumar Mahato
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Pawan K Jayaswal
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - U B Angadi
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India
| | - Neeraj Kumar
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India
| | - Nimisha Sharma
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anand K Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Jai Prakash
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - S K Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Kasim Khan
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
| | - Rupesh K Mishra
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
| | - Shailendra Rajan
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
| | - Anju Bajpai
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
| | - B S Sandhya
- ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | | | - K V Ravishankar
- ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | - M R Dinesh
- ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India.
| | - Tilak R Sharma
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Nagendra K Singh
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
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Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney RK, He Z. Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives. MOLECULAR PLANT 2017; 10:1047-1064. [PMID: 28669791 DOI: 10.1016/j.molp.2017.06.008] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/29/2017] [Accepted: 06/19/2017] [Indexed: 05/18/2023]
Abstract
There is a rapidly rising trend in the development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop molecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype-phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.
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Affiliation(s)
- Awais Rasheed
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Awais Khan
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY, USA
| | - Yunbi Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China.
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Zhao Y, Su K, Wang G, Zhang L, Zhang J, Li J, Guo Y. High-Density Genetic Linkage Map Construction and Quantitative Trait Locus Mapping for Hawthorn (Crataegus pinnatifida Bunge). Sci Rep 2017; 7:5492. [PMID: 28710433 PMCID: PMC5511184 DOI: 10.1038/s41598-017-05756-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 06/14/2017] [Indexed: 11/30/2022] Open
Abstract
Genetic linkage maps are an important tool in genetic and genomic research. In this study, two hawthorn cultivars, Qiujinxing and Damianqiu, and 107 progenies from a cross between them were used for constructing a high-density genetic linkage map using the 2b-restriction site-associated DNA (2b-RAD) sequencing method, as well as for mapping quantitative trait loci (QTL) for flavonoid content. In total, 206,411,693 single-end reads were obtained, with an average sequencing depth of 57× in the parents and 23× in the progeny. After quality trimming, 117,896 high-quality 2b-RAD tags were retained, of which 42,279 were polymorphic; of these, 12,951 markers were used for constructing the genetic linkage map. The map contained 17 linkage groups and 3,894 markers, with a total map length of 1,551.97 cM and an average marker interval of 0.40 cM. QTL mapping identified 21 QTLs associated with flavonoid content in 10 linkage groups, which explained 16.30-59.00% of the variance. This is the first high-density linkage map for hawthorn, which will serve as a basis for fine-scale QTL mapping and marker-assisted selection of important traits in hawthorn germplasm and will facilitate chromosome assignment for hawthorn whole-genome assemblies in the future.
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Affiliation(s)
- Yuhui Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Gang Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Liping Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Jijun Zhang
- College of Horticulture Sciences & Technology, Hebei Normal University of Science & Technology, Qinhuangdao, China.
| | - Junpeng Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China.
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Moon S, Lee HY, Shim D, Kim M, Ka KH, Ryoo R, Ko HG, Koo CD, Chung JW, Ryu H. Development and Molecular Characterization of Novel Polymorphic Genomic DNA SSR Markers in Lentinula edodes. MYCOBIOLOGY 2017; 45:105-109. [PMID: 28781544 PMCID: PMC5541145 DOI: 10.5941/myco.2017.45.2.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/03/2017] [Accepted: 06/12/2017] [Indexed: 05/15/2023]
Abstract
Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.
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Affiliation(s)
- Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea
| | - Hwa-Yong Lee
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea
| | - Donghwan Shim
- Division of Forest Genetic Resources, National Institute of Forest Science, Suwon 16631, Korea
| | - Myungkil Kim
- Division of Wood Chemistry & Microbiology, National Institute of Forest Science, Seoul 02455, Korea
| | - Kang-Hyeon Ka
- Division of Wood Chemistry & Microbiology, National Institute of Forest Science, Seoul 02455, Korea
| | - Rhim Ryoo
- Division of Wood Chemistry & Microbiology, National Institute of Forest Science, Seoul 02455, Korea
| | - Han-Gyu Ko
- Forest Mushroom Research Center, National Forestry Cooperative Federation, Yeoju 12653, Korea
| | - Chang-Duck Koo
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea
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Evangelisti E, Gogleva A, Hainaux T, Doumane M, Tulin F, Quan C, Yunusov T, Floch K, Schornack S. Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors. BMC Biol 2017; 15:39. [PMID: 28494759 PMCID: PMC5427549 DOI: 10.1186/s12915-017-0379-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 04/24/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plant-pathogenic oomycetes are responsible for economically important losses in crops worldwide. Phytophthora palmivora, a tropical relative of the potato late blight pathogen, causes rotting diseases in many tropical crops including papaya, cocoa, oil palm, black pepper, rubber, coconut, durian, mango, cassava and citrus. Transcriptomics have helped to identify repertoires of host-translocated microbial effector proteins which counteract defenses and reprogram the host in support of infection. As such, these studies have helped in understanding how pathogens cause diseases. Despite the importance of P. palmivora diseases, genetic resources to allow for disease resistance breeding and identification of microbial effectors are scarce. RESULTS We employed the model plant Nicotiana benthamiana to study the P. palmivora root infections at the cellular and molecular levels. Time-resolved dual transcriptomics revealed different pathogen and host transcriptome dynamics. De novo assembly of P. palmivora transcriptome and semi-automated prediction and annotation of the secretome enabled robust identification of conserved infection-promoting effectors. We show that one of them, REX3, suppresses plant secretion processes. In a survey for early transcriptionally activated plant genes we identified a N. benthamiana gene specifically induced at infected root tips that encodes a peptide with danger-associated molecular features. CONCLUSIONS These results constitute a major advance in our understanding of P. palmivora diseases and establish extensive resources for P. palmivora pathogenomics, effector-aided resistance breeding and the generation of induced resistance to Phytophthora root infections. Furthermore, our approach to find infection-relevant secreted genes is transferable to other pathogen-host interactions and not restricted to plants.
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Affiliation(s)
| | - Anna Gogleva
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
| | - Thomas Hainaux
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
- Present address: Université Libre de Bruxelles, Bruxelles, Belgium
| | - Mehdi Doumane
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
- Present address: École Normale Supérieure de Lyon, Lyon, France
| | - Frej Tulin
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
| | - Clément Quan
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
| | - Temur Yunusov
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
| | - Kévin Floch
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
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Hewitt S, Kilian B, Hari R, Koepke T, Sharpe R, Dhingra A. Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry ( Prunus avium L.). Comput Struct Biotechnol J 2017; 15:290-298. [PMID: 28392892 PMCID: PMC5376269 DOI: 10.1016/j.csbj.2017.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/02/2017] [Accepted: 03/08/2017] [Indexed: 11/25/2022] Open
Abstract
Identification of genetic polymorphisms and subsequent development of molecular markers is important for marker assisted breeding of superior cultivars of economically important species. Sweet cherry (Prunus avium L.) is an economically important non-climacteric tree fruit crop in the Rosaceae family and has undergone a genetic bottleneck due to breeding, resulting in limited genetic diversity in the germplasm that is utilized for breeding new cultivars. Therefore, it is critical to recognize the best platforms for identifying genome-wide polymorphisms that can help identify, and consequently preserve, the diversity in a genetically constrained species. For the identification of polymorphisms in five closely related genotypes of sweet cherry, a gel-based approach (TRAP), reduced representation sequencing (TRAPseq), a 6k cherry SNParray, and whole genome sequencing (WGS) approaches were evaluated in the identification of genome-wide polymorphisms in sweet cherry cultivars. All platforms facilitated detection of polymorphisms among the genotypes with variable efficiency. In assessing multiple SNP detection platforms, this study has demonstrated that a combination of appropriate approaches is necessary for efficient polymorphism identification, especially between closely related cultivars of a species. The information generated in this study provides a valuable resource for future genetic and genomic studies in sweet cherry, and the insights gained from the evaluation of multiple approaches can be utilized for other closely related species with limited genetic diversity in the breeding germplasm.
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Affiliation(s)
- Seanna Hewitt
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Benjamin Kilian
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Ramyya Hari
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Tyson Koepke
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Richard Sharpe
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Amit Dhingra
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
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Factor VIII mutation spectrum in haemophilia A patients in the population of Henan, China. Blood Coagul Fibrinolysis 2017; 28:509-513. [PMID: 28252515 DOI: 10.1097/mbc.0000000000000628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
: Defects in the coagulation factor VIII gene cause haemophilia A, which is the most common X-linked recessive bleeding disorder. In total, 45 affected families were investigated to elucidate the factor VIII gene mutation spectrum. The families were subjected to clinical, biochemical, and molecular analyses. Inverse-shifting PCR was first applied to severe haemophilia A patients to identify inversions in introns 22 and 1. Then, next-generation sequencing was performed to detect mutations in inversion-negative patients with severe haemophilia A and moderate-mild haemophilia A patients. Finally, multiplex ligation-dependent probe amplification was utilized to identify rare cases with large fragment duplications or deletions in the factor VIII gene. In total, 41 mutations were identified, 19 of which (c.24C>A, c.49T>C, c.170_171delTT, c.533T>C, c.1126delG, c.1495delA, c.1660A>C, c.1736A>G, c.2711-2712insAATCT, c.3077C>G, c.3846delA, c.4238C>G, c.4349delG, c.4828G>C, c.5821A>C, c.6190C>T, c.6656T>C, c.6902T>G, and c.1904-2A>T) were novel and 80% (44/55) of the pathogenic mutations fell into the categories of missense (43.6%), nonsense (16.36%), frameshift (14.55%), and splice (5.45%) mutations. Additionally, 10 (18.18%) patients displayed inversions in intron 22 or 1 and one case (1.82%) exhibited a 3059-bp large fragment deletion in factor VIII. This study aimed to provide insight contributing to the genetic diagnosis of haemophilia A and to fill gaps in the factor VIII mutation spectrum in northern China.
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Ren Y, Singh RP, Basnet BR, Lan CX, Huerta-Espino J, Lagudah ES, Ponce-Molina LJ. Identification and Mapping of Adult Plant Resistance Loci to Leaf Rust and Stripe Rust in Common Wheat Cultivar Kundan. PLANT DISEASE 2017; 101:456-463. [PMID: 30677352 DOI: 10.1094/pdis-06-16-0890-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Leaf rust (LR) and stripe rust (YR) are important diseases of wheat worldwide. We used 148 recombinant inbred lines (RIL) from the cross of Avocet × Kundan for determining and mapping the genetic basis of adult plant resistance (APR) loci. The population was phenotyped LR and YR for three seasons in field trials conducted in Mexico and genotyped with the diversity arrays technology sequencing (DArT-Seq) and simple sequence repeat markers. The final genetic map was constructed using 2,937 polymorphic markers with an average distance of 1.29 centimorgans between markers. Inclusive composite interval mapping identified two co-located APR quantitative trait loci (QTL) for LR and YR, two LR QTL, and three YR QTL. The co-located resistance QTL on chromosome 1BL corresponded to the pleiotropic APR gene Lr46/Yr29. QLr.cim-2BL, QYr.cim-2AL, and QYr.cim-5AS could be identified as new resistance loci in this population. Lr46/Yr29 contributed 49.5 to 65.1 and 49.2 to 66.1% of LR and YR variations, respectively. The additive interaction between detected QTL showed that LR severities for RIL combining four QTL ranged between 5.3 and 25.8%, whereas the lowest YR severities were for RIL carrying QTL on chromosomes 1BL + 2AL + 6AL. The high-density DArT-Seq markers across chromosomes can be used in fine mapping of the targeted loci and development SNP markers.
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Affiliation(s)
- Y Ren
- Mianyang Institute of Agricultural Science/Mianyang Branch of National Wheat Improvement Center, Mianyang 621023, Sichuan, China
| | - R P Singh
- International Maize and Wheat Improvement Center (CIMMYT), 06600 México D.F., Mexico
| | - B R Basnet
- International Maize and Wheat Improvement Center (CIMMYT), 06600 México D.F., Mexico
| | - C X Lan
- International Maize and Wheat Improvement Center (CIMMYT), 06600 México D.F., Mexico
| | - J Huerta-Espino
- Campo Experimental Valle de México INIFAP, 56230 Chapingo, Edo. de México, Mexico
| | - E S Lagudah
- CSIRO Agriculture, Canberra, ACT 2601, Australia
| | - L J Ponce-Molina
- National Institute of Agricultural and Livestock Researches (INIAP-Ecuador), Santa Catalina Experimental Station, Quito, Ecuador
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Teng C, Du D, Xiao L, Yu Q, Shang G, Zhao Z. Mapping and Identifying a Candidate Gene ( Bnmfs) for Female-Male Sterility through Whole-Genome Resequencing and RNA-Seq in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2017; 8:2086. [PMID: 29326731 PMCID: PMC5733364 DOI: 10.3389/fpls.2017.02086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/22/2017] [Indexed: 05/03/2023]
Abstract
In oilseed crops, carpel and stamen development play vital roles in pollination and rapeseed yield, but the genetic mechanisms underlying carpel and stamen development remain unclear. Herein, a male- and female-sterile mutant was obtained in offspring of a (Brassica napus cv. Qingyou 14) × (Qingyou 14 × B. rapa landrace Dahuang) cross. Subsequently, F2-F9 populations were generated through selfing of the heterozygote plants among the progeny of each generation. The male- and female-sterility exhibited stable inheritance in successive generations and was controlled by a recessive gene. The mutant kept the same chromosome number (2n = 38) as B. napus parent but showed abnormal meiosis for male and female. One candidate gene for the sterility was identified by simple sequence repeat (SSR) and insertion deletion length polymorphism (InDel) markers in F7-F9 plants, and whole-genome resequencing with F8 pools and RNA sequencing with F9 pools. Whole-genome resequencing found three candidate intervals (35.40-35.68, 35.74-35.75, and 45.34-46.45 Mb) on chromosome C3 in B. napus and candidate region for Bnmfs was narrowed to approximately 1.11-Mb (45.34-46.45 M) by combining SSR and InDel marker analyses with whole-genome resequencing. From transcriptome profiling in 0-2 mm buds, all of the genes in the candidate interval were detected, and only two genes with significant differences (BnaC03g56670D and BnaC03g56870D) were revealed. BnaC03g56870D was a candidate gene that shared homology with the CYP86C4 gene of Arabidopsis thaliana. Quantitative reverse transcription (qRT)-PCR analysis showed that Bnmfs primarily functioned in flower buds. Thus, sequencing and expression analyses provided evidence that BnaC03g56870D was the candidate gene for male and female sterility in the B. napus mutant.
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Bhat JA, Ali S, Salgotra RK, Mir ZA, Dutta S, Jadon V, Tyagi A, Mushtaq M, Jain N, Singh PK, Singh GP, Prabhu KV. Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding. Front Genet 2016; 7:221. [PMID: 28083016 PMCID: PMC5186759 DOI: 10.3389/fgene.2016.00221] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 12/12/2016] [Indexed: 12/31/2022] Open
Abstract
Genomic selection (GS) is a promising approach exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. In plant breeding, it provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost-benefit balance was an important consideration for GS to work in crop plants. Availability of genome-wide high-throughput, cost-effective and flexible markers, having low ascertainment bias, suitable for large population size as well for both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species. These factors were the major limitations to earlier marker systems viz., SSR and array-based, and was unimaginable before the availability of next-generation sequencing (NGS) technologies which have provided novel SNP genotyping platforms especially the genotyping by sequencing. These marker technologies have changed the entire scenario of marker applications and made the use of GS a routine work for crop improvement in both model and non-model crop species. The NGS-based genotyping have increased genomic-estimated breeding value prediction accuracies over other established marker platform in cereals and other crop species, and made the dream of GS true in crop breeding. But to harness the true benefits from GS, these marker technologies will be combined with high-throughput phenotyping for achieving the valuable genetic gain from complex traits. Moreover, the continuous decline in sequencing cost will make the WGS feasible and cost effective for GS in near future. Till that time matures the targeted sequencing seems to be more cost-effective option for large scale marker discovery and GS, particularly in case of large and un-decoded genomes.
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Affiliation(s)
- Javaid A Bhat
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - Sajad Ali
- National Research Centre for Plant Biotechnology New Delhi, India
| | - Romesh K Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu Chatha, India
| | - Zahoor A Mir
- National Research Centre for Plant Biotechnology New Delhi, India
| | - Sutapa Dutta
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - Vasudha Jadon
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - Anshika Tyagi
- National Research Centre for Plant Biotechnology New Delhi, India
| | - Muntazir Mushtaq
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu Chatha, India
| | - Neelu Jain
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - Pradeep K Singh
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - Gyanendra P Singh
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - K V Prabhu
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
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Wang Y, Xiao L, Guo S, An F, Du D. Fine Mapping and Whole-Genome Resequencing Identify the Seed Coat Color Gene in Brassica rapa. PLoS One 2016; 11:e0166464. [PMID: 27829069 PMCID: PMC5102352 DOI: 10.1371/journal.pone.0166464] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 10/28/2016] [Indexed: 11/19/2022] Open
Abstract
A yellow seed coat is a desirable agronomic trait in the seeds of oilseed-type Brassica crops. In this study, we identified a candidate gene for seed coat color in Dahuang, a landrace of Brassica rapa. A previous study of Dahuang mapped the seed coat color gene Brsc1 to a 2.8-Mb interval on chromosome A9 of B. rapa. In the present study, the density of the linkage map for Brsc1 was increased by adding simple sequence repeat (SSR) markers, and the candidate region for Brsc1 was narrowed to 1.04 Mb. In addition, whole-genome resequencing with bulked segregant analysis (BSA) was conducted to identify candidate intervals for Brsc1. A genome-wide comparison of SNP profiles was performed between yellow-seeded and brown-seeded bulk samples. SNP index analyses identified a major candidate interval on chromosome A9 (A09:18,255,838-18,934,000, 678 kb) containing a long overlap with the target region recovered from the fine mapping results. According to gene annotation, Bra028067 (BrTT1) is an important candidate gene for Brsc1 in the overlapping region. Quantitative reverse transcription (qRT)-PCR revealed that BrTT1 mainly functions in the seed. Point mutations and small deletions in BrTT1 were found between yellow- and brown-seeded Dahuang plants. Collectively, the expression and sequence analysis results provide preliminary evidence that BrTT1 is a candidate gene for the seed coat color trait in Dahuang.
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Affiliation(s)
- Yanhua Wang
- Key Laboratory of Spring Rapeseed Genetic Improvement, The Qinghai Research Branch of the National Rapeseed Genetic Improvement Center, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
| | - Lu Xiao
- Key Laboratory of Spring Rapeseed Genetic Improvement, The Qinghai Research Branch of the National Rapeseed Genetic Improvement Center, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
| | - Shaomin Guo
- Key Laboratory of Spring Rapeseed Genetic Improvement, The Qinghai Research Branch of the National Rapeseed Genetic Improvement Center, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
| | - Fengyun An
- Key Laboratory of Spring Rapeseed Genetic Improvement, The Qinghai Research Branch of the National Rapeseed Genetic Improvement Center, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
| | - Dezhi Du
- Key Laboratory of Spring Rapeseed Genetic Improvement, The Qinghai Research Branch of the National Rapeseed Genetic Improvement Center, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- * E-mail:
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Yu F, Zhang X, Huang Z, Chu M, Song T, Falk KC, Deora A, Chen Q, Zhang Y, McGregor L, Gossen BD, McDonald MR, Peng G. Identification of Genome-Wide Variants and Discovery of Variants Associated with Brassica rapa Clubroot Resistance Gene Rcr1 through Bulked Segregant RNA Sequencing. PLoS One 2016; 11:e0153218. [PMID: 27078023 DOI: 10.1371/journal.pone.00153218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/27/2016] [Indexed: 05/26/2023] Open
Abstract
Clubroot, caused by Plasmodiophora brassicae, is an important disease on Brassica species worldwide. A clubroot resistance gene, Rcr1, with efficacy against pathotype 3 of P. brassicae, was previously mapped to chromosome A03 of B. rapa in pak choy cultivar "Flower Nabana". In the current study, resistance to pathotypes 2, 5 and 6 was shown to be associated with Rcr1 region on chromosome A03. Bulked segregant RNA sequencing was performed and short read sequences were assembled into 10 chromosomes of the B. rapa reference genome v1.5. For the resistant (R) bulks, a total of 351.8 million (M) sequences, 30,836.5 million bases (Mb) in length, produced 120-fold coverage of the reference genome. For the susceptible (S) bulks, 322.9 M sequences, 28,216.6 Mb in length, produced 109-fold coverage. In total, 776.2 K single nucleotide polymorphisms (SNPs) and 122.2 K insertion / deletion (InDels) in R bulks and 762.8 K SNPs and 118.7 K InDels in S bulks were identified; each chromosome had about 87% SNPs and 13% InDels, with 78% monomorphic and 22% polymorphic variants between the R and S bulks. Polymorphic variants on each chromosome were usually below 23%, but made up 34% of the variants on chromosome A03. There were 35 genes annotated in the Rcr1 target region and variants were identified in 21 genes. The numbers of poly variants differed significantly among the genes. Four out of them encode Toll-Interleukin-1 receptor / nucleotide-binding site / leucine-rich-repeat proteins; Bra019409 and Bra019410 harbored the higher numbers of polymorphic variants, which indicates that they are more likely candidates of Rcr1. Fourteen SNP markers in the target region were genotyped using the Kompetitive Allele Specific PCR method and were confirmed to associate with Rcr1. Selected SNP markers were analyzed with 26 recombinants obtained from a segregating population consisting of 1587 plants, indicating that they were completely linked to Rcr1. Nine SNP markers were used for marker-assisted introgression of Rcr1 into B. napus canola from B. rapa, with 100% accuracy in this study.
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Affiliation(s)
- Fengqun Yu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Xingguo Zhang
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Zhen Huang
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Mingguang Chu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Tao Song
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Kevin C Falk
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Abhinandan Deora
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
| | - Qilin Chen
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Yan Zhang
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Linda McGregor
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Bruce D Gossen
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Mary Ruth McDonald
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
| | - Gary Peng
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
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Identification of Genome-Wide Variants and Discovery of Variants Associated with Brassica rapa Clubroot Resistance Gene Rcr1 through Bulked Segregant RNA Sequencing. PLoS One 2016; 11:e0153218. [PMID: 27078023 PMCID: PMC4831815 DOI: 10.1371/journal.pone.0153218] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/27/2016] [Indexed: 11/19/2022] Open
Abstract
Clubroot, caused by Plasmodiophora brassicae, is an important disease on Brassica species worldwide. A clubroot resistance gene, Rcr1, with efficacy against pathotype 3 of P. brassicae, was previously mapped to chromosome A03 of B. rapa in pak choy cultivar “Flower Nabana”. In the current study, resistance to pathotypes 2, 5 and 6 was shown to be associated with Rcr1 region on chromosome A03. Bulked segregant RNA sequencing was performed and short read sequences were assembled into 10 chromosomes of the B. rapa reference genome v1.5. For the resistant (R) bulks, a total of 351.8 million (M) sequences, 30,836.5 million bases (Mb) in length, produced 120-fold coverage of the reference genome. For the susceptible (S) bulks, 322.9 M sequences, 28,216.6 Mb in length, produced 109-fold coverage. In total, 776.2 K single nucleotide polymorphisms (SNPs) and 122.2 K insertion / deletion (InDels) in R bulks and 762.8 K SNPs and 118.7 K InDels in S bulks were identified; each chromosome had about 87% SNPs and 13% InDels, with 78% monomorphic and 22% polymorphic variants between the R and S bulks. Polymorphic variants on each chromosome were usually below 23%, but made up 34% of the variants on chromosome A03. There were 35 genes annotated in the Rcr1 target region and variants were identified in 21 genes. The numbers of poly variants differed significantly among the genes. Four out of them encode Toll-Interleukin-1 receptor / nucleotide-binding site / leucine-rich-repeat proteins; Bra019409 and Bra019410 harbored the higher numbers of polymorphic variants, which indicates that they are more likely candidates of Rcr1. Fourteen SNP markers in the target region were genotyped using the Kompetitive Allele Specific PCR method and were confirmed to associate with Rcr1. Selected SNP markers were analyzed with 26 recombinants obtained from a segregating population consisting of 1587 plants, indicating that they were completely linked to Rcr1. Nine SNP markers were used for marker-assisted introgression of Rcr1 into B. napus canola from B. rapa, with 100% accuracy in this study.
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Zhang Z, Shang H, Shi Y, Huang L, Li J, Ge Q, Gong J, Liu A, Chen T, Wang D, Wang Y, Palanga KK, Muhammad J, Li W, Lu Q, Deng X, Tan Y, Song W, Cai J, Li P, Rashid HO, Gong W, Yuan Y. Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.). BMC PLANT BIOLOGY 2016; 16:79. [PMID: 27067834 PMCID: PMC4827241 DOI: 10.1186/s12870-016-0741-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/17/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping. RESULTS In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0-153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37 cM with an average marker interval of 0.78 cM without gaps larger than 10 cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15-16.70 % of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis. CONCLUSIONS This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection.
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Affiliation(s)
- Zhen Zhang
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Haihong Shang
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Yuzhen Shi
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Long Huang
- />Biomarker Technologies Corporation, Beijing, 103100 China
| | - Junwen Li
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Qun Ge
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Juwu Gong
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Aiying Liu
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Tingting Chen
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Dan Wang
- />Biomarker Technologies Corporation, Beijing, 103100 China
| | - Yanling Wang
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Koffi Kibalou Palanga
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Jamshed Muhammad
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Weijie Li
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Quanwei Lu
- />Anyang Institute of Technology, Anyang, 455000 Henan China
| | - Xiaoying Deng
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Yunna Tan
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Weiwu Song
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Juan Cai
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Pengtao Li
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Harun or Rashid
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Wankui Gong
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Youlu Yuan
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
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Kang YJ, Lee T, Lee J, Shim S, Jeong H, Satyawan D, Kim MY, Lee SH. Translational genomics for plant breeding with the genome sequence explosion. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1057-69. [PMID: 26269219 PMCID: PMC5042036 DOI: 10.1111/pbi.12449] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/04/2015] [Accepted: 07/10/2015] [Indexed: 05/22/2023]
Abstract
The use of next-generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.
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Affiliation(s)
- Yang Jae Kang
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Taeyoung Lee
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Jayern Lee
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Sangrea Shim
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Haneul Jeong
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Dani Satyawan
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
- Indonesian Center for Agricultural Biotechnology and Genomic resources Research and Development (ICABIOGRAD-IAARD), Bogor, Indonesia
| | - Moon Young Kim
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Suk-Ha Lee
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding. PLoS One 2016; 11:e0147187. [PMID: 26799713 PMCID: PMC4723255 DOI: 10.1371/journal.pone.0147187] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 12/30/2015] [Indexed: 11/19/2022] Open
Abstract
Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genome-wide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection.
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49
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Recent advances in molecular marker techniques: Insight into QTL mapping, GWAS and genomic selection in plants. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s12892-015-0037-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Saeed AF, Wang R, Wang S. Microsatellites in Pursuit of Microbial Genome Evolution. Front Microbiol 2016; 6:1462. [PMID: 26779133 PMCID: PMC4700210 DOI: 10.3389/fmicb.2015.01462] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 12/07/2015] [Indexed: 12/27/2022] Open
Abstract
Microsatellites or short sequence repeats are widespread genetic markers which are hypermutable 1-6 bp long short nucleotide motifs. Significantly, their applications in genetics are extensive due to their ceaseless mutational degree, widespread length variations and hypermutability skills. These features make them useful in determining the driving forces of evolution by using powerful molecular techniques. Consequently, revealing important questions, for example, what is the significance of these abundant sequences in DNA, what are their roles in genomic evolution? The answers of these important questions are hidden in the ways these short motifs contributed in altering the microbial genomes since the origin of life. Even though their size ranges from 1 -to- 6 bases, these repeats are becoming one of the most popular genetic probes in determining their associations and phylogenetic relationships in closely related genomes. Currently, they have been widely used in molecular genetics, biotechnology and evolutionary biology. However, due to limited knowledge; there is a significant gap in research and lack of information concerning hypermutational mechanisms. These mechanisms play a key role in microsatellite loci point mutations and phase variations. This review will extend the understandings of impacts and contributions of microsatellite in genomic evolution and their universal applications in microbiology.
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Affiliation(s)
- Abdullah F. Saeed
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
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