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Tosi L, Chaikban L, Larman BH, Rosenfield J, Parekkadan B. Massively parallel DNA target capture using long adapter single stranded oligonucleotide (LASSO) probes assembled through a novel DNA recombinase mediated methodology. Biotechnol J 2022; 17:e2100240. [PMID: 34775678 PMCID: PMC8825753 DOI: 10.1002/biot.202100240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 02/03/2023]
Abstract
In the attempt to bridge the widening gap from DNA sequence to biological function, we developed a novel methodology to assemble Long-Adapter Single-Strand Oligonucleotide (LASSO) probe libraries that enabled the massively multiplexed capture of kilobase-sized DNA fragments for downstream long read DNA sequencing or expression. This method uses short DNA oligonucleotides (pre-LASSO probes) and a plasmid vector that supplies the linker sequence for the mature LASSO probe through Cre-LoxP intramolecular recombination. This strategy generates high quality LASSO probes libraries (≈46% of correct probes). We performed NGS analysis of the post-capture PCR amplification of DNA circles obtained from the LASSO capture of 3087 Escherichia coli ORFs spanning from 400- to 5000 bp. The median enrichment of all targeted ORFs versus untargeted ORFs was 30 times. For ORFs up to 1kb in size, targeted ORFs were enriched up to a median of 260-fold. Here, we show that LASSO probes obtained in this manner, were able to capture full-length open reading frames from total human cDNA. Furthermore, we show that the LASSO capture specificity and sensitivity is sufficient for target capture from total human genomic DNA template. This technology can be used for the preparation of long-read sequencing libraries and for massively multiplexed cloning of human sequences.
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Affiliation(s)
- Lorenzo Tosi
- Department of Biomedical Engineering, Rutgers University,
Piscataway, New Jersey 08854, USA
| | - Lamia Chaikban
- Department of Biomedical Engineering, Rutgers University,
Piscataway, New Jersey 08854, USA
| | - Benjamin H. Larman
- Institute of Cell Engineering, Division of Immunology,
Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey Rosenfield
- Cancer Institute of New Jersey, New Brunswick, New Jersey
08854, USA,Department of Pathology, Robert Wood Johnson Medical
School, New Brunswick, NJ 08903, USA
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers University,
Piscataway, New Jersey 08854, USA,Cancer Institute of New Jersey, New Brunswick, New Jersey
08854, USA,Correspondence and requests for materials should
be addressed to B.P. (; 599 Taylor
Road, Piscataway, NJ 08854)
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Li P, Su T, Zhang B, Li P, Xin X, Yue X, Cao Y, Wang W, Zhao X, Yu Y, Zhang D, Yu S, Zhang F. Identification and fine mapping of qSB.A09, a major QTL that controls shoot branching in Brassica rapa ssp. chinensis Makino. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1055-1068. [PMID: 31919538 DOI: 10.1007/s00122-020-03531-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
QTL mapping plus bulked segregant analysis revealed a major QTL for shoot branching in non-heading Chinese cabbage. The candidate gene was then identified using sequence alignment and expression analysis. Shoot branching is a complex quantitative trait that contributes to plant architecture and ultimately yield. Although many studies have examined branching in grain crops, the genetic control of shoot branching in vegetable crops such as Brassica rapa L. ssp. chinensis remains poorly understood. In this study, we used bulked segregant analysis (BSA) of an F2 population to detect a major quantitative trait locus (QTL) for shoot branching, designated shoot branching 9 (qSB.A09) on the long arm of chromosome A09 in Brassica rapa L. ssp. chinensis. In addition, traditional QTL mapping of the F2 population revealed six QTLs in different regions. Of these, the mapping region on chromosome A09 was consistent with the results of BSA-seq analysis, as well as being stable over the 2-year study period, explaining 19.37% and 22.18% of the phenotypic variation across multiple genetic backgrounds. Using extreme recombinants, qSB.A09 was further delimited to a 127-kb genomic region harboring 28 annotated genes. We subsequently identified the GRAS transcription factor gene Bra007056 as a potential candidate gene; Bra007056 is an ortholog of MONOCULM 1 (MOC1), the key gene that controls tillering in rice. Quantitative RT-PCR further revealed that expression of Bra007056 was positively correlated with the shoot branching phenotype. Furthermore, an insertion/deletion marker specific to Bra007056 co-segregated with the shoot branching trait in the F2 populations. Overall, these results provide the basis for elucidating the molecular mechanism of shoot branching in Brassica rapa ssp. chinensis Makino.
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Affiliation(s)
- Pan Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Tongbing Su
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Bin Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Peirong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Xiaoyun Xin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Xiaozhen Yue
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Yunyun Cao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, 100097, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China.
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, 100097, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China.
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Yang M, Huang C, Wang M, Fan H, Wan S, Wang Y, He J, Guan R. Fine mapping of an up-curling leaf locus (BnUC1) in Brassica napus. BMC PLANT BIOLOGY 2019; 19:324. [PMID: 31324149 PMCID: PMC6642557 DOI: 10.1186/s12870-019-1938-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/11/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Leaf shape development research is important because leaf shapes such as moderate curling can help to improve light energy utilization efficiency. Leaf growth and development includes initiation of the leaf primordia and polar differentiation of the proximal-distal, adaxial-abaxial, and centrolateral axes. Changes in leaf adaxial-abaxial polarity formation, auxin synthesis and signaling pathways, and development of sclerenchyma and cuticle can cause abnormal leaf shapes such as up-curling leaf. Although many genes related to leaf shape development have been reported, the detailed mechanism of leaf development is still unclear. Here, we report an up-curling leaf mutant plant from our Brassica napus germplasm. We studied its inheritance, mapped the up-curling leaf locus BnUC1, built near-isogenic lines for the Bnuc1 mutant, and evaluated the effect of the dominant leaf curl locus on leaf photosynthetic efficiency and agronomic traits. RESULTS The up-curling trait was controlled by one dominant locus in a progeny population derived from NJAU5734 and Zhongshuang 11 (ZS11). This BnUC1 locus was mapped in an interval of 2732.549 kb on the A05 chromosome of B. napus using Illumina Brassica 60 K Bead Chip Array. To fine map BnUC1, we designed 201 simple sequence repeat (SSR) primers covering the mapping interval. Among them, 16 polymorphic primers that narrowed the mapping interval to 54.8 kb were detected using a BC6F2 family population with 654 individuals. We found six annotated genes in the mapping interval using the B. napus reference genome, including BnaA05g18250D and BnaA05g18290D, which bioinformatics and gene expression analyses predicted may be responsible for leaf up-curling. The up-curling leaf trait had negative effects on the agronomic traits of 30 randomly selected individuals from the BC6F2 population. The near-isogenic line of the up-curling leaf (ZS11-UC1) was constructed to evaluate the effect of BnUC1 on photosynthetic efficiency. The results indicated that the up-curling leaf trait locus was beneficial to improve the photosynthetic efficiency. CONCLUSIONS An up-curling leaf mutant Bnuc1 was controlled by one dominant locus BnUC1. This locus had positive effects on photosynthetic efficiency, negative effects on some agronomic traits, and may help to increase planting density in B. napus.
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Affiliation(s)
- Mao Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Chengwei Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Mingming Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Hao Fan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shubei Wan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yangming Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jianbo He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Rongzhan Guan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
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Sharma D, Tiwari A, Sood S, Jamra G, Singh NK, Meher PK, Kumar A. Genome wide association mapping of agro-morphological traits among a diverse collection of finger millet (Eleusine coracana L.) genotypes using SNP markers. PLoS One 2018; 13:e0199444. [PMID: 30092057 PMCID: PMC6084814 DOI: 10.1371/journal.pone.0199444] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 06/07/2018] [Indexed: 11/19/2022] Open
Abstract
Finger millet (Eleusine coracana L.) is an important dry-land cereal in Asia and Africa because of its ability to provide assured harvest under extreme dry conditions and excellent nutritional properties. However, the genetic improvement of the crop is lacking in the absence of suitable genomic resources for reliable genotype-phenotype associations. Keeping this in view, a diverse global finger millet germplasm collection of 113 accessions was evaluated for 14 agro-morphological characters in two environments viz. ICAR-Vivekananda Institute of Hill Agriculture, Almora (E1) and Crop Research Centre (CRC), GBPUA&T, Pantnagar (E2), India. Principal component analysis and cluster analysis of phenotypic data separated the Indian and exotic accessions into two separate groups. Previously generated SNPs through genotyping by sequencing (GBS) were used for association mapping to identify reliable marker(s) linked to grain yield and its component traits. The marker trait associations were determined using single locus single trait (SLST), multi-locus mixed model (MLMM) and multi-trait mixed model (MTMM) approaches. SLST led to the identification of 20 marker-trait associations (MTAs) (p value<0.01 and <0.001) for 5 traits. While advanced models, MLMM and MTMM resulted in additional 36 and 53 MTAs, respectively. Nine MTAs were common out of total 109 associations in all the three mapping approaches (SLST, MLMM and MTMM). Among these nine SNPs, five SNP sequences showed homology to candidate genes of Oryza sativa (Rice) and Setaria italica (Foxtail millet), which play an important role in flowering, maturity and grain yield. In addition, 67 and 14 epistatic interactions were identified for 10 and 7 traits at E1 and E2 locations, respectively. Hence, the 109 novel SNPs associated with important agro-morphological traits, reported for the first time in this study could be precisely utilized in finger millet genetic improvement after validation.
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Affiliation(s)
- Divya Sharma
- Department of Molecular Biology & Genetic Engineering, G.B. Pant Univ. of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Apoorv Tiwari
- Department of Molecular Biology & Genetic Engineering, G.B. Pant Univ. of Agriculture and Technology, Pantnagar, Uttarakhand, India
- Sam Higginbottom University of Agriculture, Technology & Sciences, Allahabad, Uttar Pradesh, India
| | - Salej Sood
- ICAR-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, India
- * E-mail: (AK); (SS)
| | - Gautam Jamra
- Department of Molecular Biology & Genetic Engineering, G.B. Pant Univ. of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - N. K. Singh
- Department of Genetics & Plant Breeding, College of Agriculture, G.B. Pant Univ. of Agriculture & Technology, Pantnagar, Uttarakhand, India
| | - Prabina Kumar Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Kumar
- Department of Molecular Biology & Genetic Engineering, G.B. Pant Univ. of Agriculture and Technology, Pantnagar, Uttarakhand, India
- * E-mail: (AK); (SS)
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Zhao J, Chen A, You X, Xu Z, Zhao Y, He W, Zhao L, Yang S. A panel of SNP markers for meat traceability of Halal beef in the Chinese market. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.11.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Adhikari S, Saha S, Biswas A, Rana TS, Bandyopadhyay TK, Ghosh P. Application of molecular markers in plant genome analysis: a review. THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0214-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Wu Q, Zhou G, Yang S, Abulikemu BT, Luo R, Zhang Y, Li X, Xu X, Li C. SNP genotyping in sheep from northwest and east China for meat traceability. J Verbrauch Lebensm 2017. [DOI: 10.1007/s00003-017-1092-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wang Y, Chen W, Chu P, Wan S, Yang M, Wang M, Guan R. Mapping a major QTL responsible for dwarf architecture in Brassica napus using a single-nucleotide polymorphism marker approach. BMC PLANT BIOLOGY 2016; 16:178. [PMID: 27538713 PMCID: PMC4991092 DOI: 10.1186/s12870-016-0865-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 08/05/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND Key genes related to plant type traits have played very important roles in the "green revolution" by increasing lodging resistance and elevating the harvest indices of crop cultivars. Although there have been numerous achievements in the development of dwarfism and plant type in Brassica napus breeding, exploring new materials conferring oilseed rape with efficient plant types that provide higher yields is still of significance in breeding, as well as in elucidating the mechanisms underlying plant development. Here, we report a new dwarf architecture with down-curved leaf mutant (Bndwf/dcl1) isolated from an ethyl methanesulphonate (EMS)-mutagenized B. napus line, together with its inheritance and gene mapping, and pleiotropic effects of the mapped locus on plant-type traits. RESULTS We constructed a high-density single-nucleotide polymorphism (SNP) map using a backcross population derived from the Bndwf/dcl1 mutant and the canola cultivar 'zhongshuang11' ('ZS11') and mapped the dwarf architecture with the down-curved leaf dominant locus, BnDWF/DCL1, in a 6.58-cM interval between SNP marker bins M46180 and M49962 on the linkage group (LG) C05 of B. napus. Further mapping with other materials derived from Bndwf/dcl1 narrowed the interval harbouring BnDWF/DCL1 to 175 kb in length and this interval contained 16 annotated genes. Quantitative trait locus (QTL) mappings with the backcross population for plant type traits, including plant height, branching height, main raceme length and average branching interval, indicated that the mapped QTLs for plant type traits were located at the same position as the BnDWF/DCL1 locus. CONCLUSIONS This study suggests that the BnDWF/DCL1 locus is a major pleiotropic locus/QTL in B. napus, which may reduce plant height, alter plant type traits and change leaf shape, and thus may lead to compact plant architecture. Accordingly, this locus may have substantial breeding potential for increasing planting density.
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Affiliation(s)
- Yankun Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu China
| | - Wenjing Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu China
| | - Pu Chu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu China
| | - Shubei Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu China
| | - Mao Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu China
| | - Mingming Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu China
| | - Rongzhan Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu China
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Fine mapping of a dominant gene conferring chlorophyll-deficiency in Brassica napus. Sci Rep 2016; 6:31419. [PMID: 27506952 PMCID: PMC4979034 DOI: 10.1038/srep31419] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 07/20/2016] [Indexed: 11/21/2022] Open
Abstract
Leaf colour regulation is important in photosynthesis and dry material production. Most of the reported chlorophyll-deficient loci are recessive. The dominant locus is rarely reported, although it may be more important than the recessive locus in the regulation of photosynthesis efficiency. During the present study, we mapped a chlorophyll-deficient dominant locus (CDE1) from the ethyl methanesulfonate-mutagenized Brassica napus line NJ7982. Using an F2 population derived from the chlorophyll-deficient mutant (cde1) and the canola variety ‘zhongshuang11’, a high-density linkage map was constructed, consisting of 19 linkage groups with 2,878 bins containing 13,347 SNP markers, with a total linkage map length of 1,968.6 cM. Next, the CDE1 locus was mapped in a 0.9-cM interval of chromosome C08 of B. napus, co-segregating with nine SNP markers. In the following fine-mapping of the gene using the inherited F2:3 populations of 620 individuals, the locus was identified in an interval with a length of 311 kb. A bioinformatics analysis revealed that the mapping interval contained 22 genes. These results produced a good foundation for continued research on the dominant locus involved in chlorophyll content regulation.
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Parida SK, Kalia S, Pandit A, Nayak P, Singh RK, Gaikwad K, Srivastava PS, Singh NK, Mohapatra T. Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane. PLANT CELL REPORTS 2016; 35:1629-1653. [PMID: 27289592 DOI: 10.1007/s00299-016-1978-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/21/2016] [Indexed: 06/06/2023]
Abstract
Single nucleotide polymorphism in sugar pathway and disease resistance genes showing genetic association with sugar content and red rot resistance would be useful in marker-assisted genetic improvement of sugarcane. Validation and genotyping of potential sequence variants in candidate genes are necessary to understand their functional significance and trait association potential. We discovered, characterized, validated and genotyped SNPs and InDels in sugar pathway and disease resistance genes of Saccharum complex and sugarcane varieties using amplicon sequencing and CAPS assays. The SNPs were abundant in the non-coding 3'UTRs than 5'UTRs and coding sequences depicting a strong bias toward C to T transition substitutions than transversions. Sequencing of cloned amplicons validated 61.6 and 45.2 % SNPs detected in silico in 21 sugar pathway and 16 disease resistance genes, respectively. Sixteen SNPs in four sugar pathway genes and 10 SNPs in nine disease resistance genes were validated through cost-effective CAPS assay. Functional and adaptive significance of SNP and protein haplotypes identified in sugar pathway and disease resistance genes was assessed by correlating their allelic variation with missense amino acid substitutions in the functional domains, alteration in protein structure models and possible modulation of catalytic enzyme activity in contrasting high and low sugar and moderately red rot resistant and highly susceptible sugarcane genotypes. A strong genetic association of five SNPs in the sugar pathway and disease resistance genes, and an InDel marker in the promoter sequence of sucrose synthase-2 gene, with sugar content and red rot resistance, was evident. The functionally relevant SNPs and InDels, detected and validated in sugar pathway and disease resistance genes, and genic CAPS markers designed, would be of immense use in marker-assisted genetic improvement of sugarcane for sugar content and disease resistance.
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Affiliation(s)
- Swarup K Parida
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sanjay Kalia
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
- Department of Biotechnology, CGO Complex, Lodhi Road, New Delhi, 110003, India
| | - Awadhesh Pandit
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
- National Centre for Biological Sciences, Bengaluru, 560065, Karnataka , India
| | - Preetam Nayak
- Utkal University, Vanivihar, Bhubaneswar, Odisha, 751004, India
| | - Ram Kushal Singh
- U.P. Council of Sugarcane Research, Shahjahanpur, Uttar Pradesh, 242001, India
| | - Kishor Gaikwad
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
| | | | - Nagendra K Singh
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
| | - Trilochan Mohapatra
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India.
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110001, India.
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11
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Wang Y, He J, Yang L, Wang Y, Chen W, Wan S, Chu P, Guan R. Fine mapping of a major locus controlling plant height using a high-density single-nucleotide polymorphism map in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1479-91. [PMID: 27147069 DOI: 10.1007/s00122-016-2718-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/19/2016] [Indexed: 05/08/2023]
Abstract
A saturated map was constructed using SNP markers to fine-map a Brassica napus dominant locus for dwarf mutant onto a 152-kb interval of chromosome A09 containing 14 genes. Major dwarf loci in crops may play important roles in crop improvement and developmental genetics. The present study investigated and fine-mapped a Brassica napus dwarf-dominant locus BnDWF1. Plants carrying the BnDWF1 locus in populations derived from 'zhongshuang11' and Bndwf1 have deep-green leaves and dwarf architecture that differ sharply from tall plants with normal green leaves. BnDWF1, as a major locus controlling plant height, showed a very high heritability (0.91-0.95). To map this locus, a high-density single-nucleotide polymorphism map was constructed, and the BnDWF1 locus was mapped at an interval between single-nucleotide polymorphism markers, M19704 and M19695, on linkage group A09 of B. napus, with five co-segregating single-nucleotide polymorphism markers. Furthermore, fine mapping narrowed the interval harboring BnDWF1 to 152 kb in length in B. napus. This interval contains 14 annotated or predicted genes, seven of which are candidates responsible for the dwarf trait. This study provides an effective foundation for the study of plant height regulation and plant type breeding in B. napus.
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Affiliation(s)
- Yankun Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Jianbo He
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Li Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Yu Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Wenjing Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Shubei Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Pu Chu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Rongzhan Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China.
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12
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Kumar A, Sharma D, Tiwari A, Jaiswal JP, Singh NK, Sood S. Genotyping-by-Sequencing Analysis for Determining Population Structure of Finger Millet Germplasm of Diverse Origins. THE PLANT GENOME 2016; 9. [PMID: 27898819 DOI: 10.3835/plantgenome2015.07.0058] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Finger millet [ (L.) Gaertn.] is grown mainly by subsistence farmers in arid and semiarid regions of the world. To broaden its genetic base and to boost its production, it is of paramount importance to characterize and genotype the diverse gene pool of this important food and nutritional security crop. However, as a result of nonavailability of the genome sequence of finger millet, the progress could not be made in realizing the molecular basis of unique qualities of the crop. In the present investigation, attempts have been made to characterize the genetically diverse collection of 113 finger millet accessions through whole-genome genotyping-by-sequencing (GBS), which resulted in a genome-wide set of 23,000 single-nucleotide polymorphisms (SNPs) segregating across the entire collection and several thousand SNPs segregating within every accession. A model-based population structure analysis reveals the presence of three subpopulations among the finger millet accessions, which are in parallel with the results of phylogenetic analysis. The observed population structure is consistent with the hypothesis that finger millet was domesticated first in Africa, and from there it was introduced to India some 3000 yr ago. A total of 1128 gene ontology (GO) terms were assigned to SNP-carrying genes for three main categories: biological process, cellular component, and molecular function. Facilitated access to high-throughput genotyping and sequencing technologies are likely to improve the breeding process in developing countries, and as such, this data will be very useful to breeders who are working for the genetic improvement of finger millet.
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13
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Structural Variation (SV) Markers in the Basidiomycete Volvariella volvacea and Their Application in the Construction of a Genetic Map. Int J Mol Sci 2015. [PMID: 26204838 PMCID: PMC4519972 DOI: 10.3390/ijms160716669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Molecular markers and genetic maps are useful tools in genetic studies. Novel molecular markers and their applications have been developed in recent years. With the recent advancements in sequencing technology, the genomic sequences of an increasingly great number of fungi have become available. A novel type of molecular marker was developed to construct the first reported linkage map of the edible and economically important basidiomycete Volvariella volvacea by using 104 structural variation (SV) markers that are based on the genomic sequences. Because of the special and simple life cycle in basidiomycete, SV markers can be effectively developed by genomic comparison and tested in single spore isolates (SSIs). This stable, convenient and rapidly developed marker may assist in the construction of genetic maps and facilitate genomic research for other species of fungi.
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Hu X, Ren J, Ren X, Huang S, Sabiel SAI, Luo M, Nevo E, Fu C, Peng J, Sun D. Association of Agronomic Traits with SNP Markers in Durum Wheat (Triticum turgidum L. durum (Desf.)). PLoS One 2015; 10:e0130854. [PMID: 26110423 PMCID: PMC4482485 DOI: 10.1371/journal.pone.0130854] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/25/2015] [Indexed: 01/11/2023] Open
Abstract
Association mapping is a powerful approach to detect associations between traits of interest and genetic markers based on linkage disequilibrium (LD) in molecular plant breeding. In this study, 150 accessions of worldwide originated durum wheat germplasm (Triticum turgidum spp. durum) were genotyped using 1,366 SNP markers. The extent of LD on each chromosome was evaluated. Association of single nucleotide polymorphisms (SNP) markers with ten agronomic traits measured in four consecutive years was analyzed under a mix linear model (MLM). Two hundred and one significant association pairs were detected in the four years. Several markers were associated with one trait, and also some markers were associated with multiple traits. Some of the associated markers were in agreement with previous quantitative trait loci (QTL) analyses. The function and homology analyses of the corresponding ESTs of some SNP markers could explain many of the associations for plant height, length of main spike, number of spikelets on main spike, grain number per plant, and 1000-grain weight, etc. The SNP associations for the observed traits are generally clustered in specific chromosome regions of the wheat genome, mainly in 2A, 5A, 6A, 7A, 1B, and 6B chromosomes. This study demonstrates that association mapping can complement and enhance previous QTL analyses and provide additional information for marker-assisted selection.
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Affiliation(s)
- Xin Hu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
| | - Jing Ren
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong, 253023, China
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
| | - Sisi Huang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
| | - Salih A. I. Sabiel
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
| | - Mingcheng Luo
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, United States of America
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 31905, Israel
| | - Chunjie Fu
- Science and Technology Center, China National Seed Group Co., Ltd, Wuhan, Hubei, 430206, China
| | - Junhua Peng
- Science and Technology Center, China National Seed Group Co., Ltd, Wuhan, Hubei, 430206, China
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, Hubei, 434025, China
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15
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Kujur A, Bajaj D, Upadhyaya HD, Das S, Ranjan R, Shree T, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea. FRONTIERS IN PLANT SCIENCE 2015; 6:162. [PMID: 25873920 PMCID: PMC4379880 DOI: 10.3389/fpls.2015.00162] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/01/2015] [Indexed: 05/19/2023]
Abstract
The genome-wide discovery and high-throughput genotyping of SNPs in chickpea natural germplasm lines is indispensable to extrapolate their natural allelic diversity, domestication, and linkage disequilibrium (LD) patterns leading to the genetic enhancement of this vital legume crop. We discovered 44,844 high-quality SNPs by sequencing of 93 diverse cultivated desi, kabuli, and wild chickpea accessions using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays that were physically mapped across eight chromosomes of desi and kabuli. Of these, 22,542 SNPs were structurally annotated in different coding and non-coding sequence components of genes. Genes with 3296 non-synonymous and 269 regulatory SNPs could functionally differentiate accessions based on their contrasting agronomic traits. A high experimental validation success rate (92%) and reproducibility (100%) along with strong sensitivity (93-96%) and specificity (99%) of GBS-based SNPs was observed. This infers the robustness of GBS as a high-throughput assay for rapid large-scale mining and genotyping of genome-wide SNPs in chickpea with sub-optimal use of resources. With 23,798 genome-wide SNPs, a relatively high intra-specific polymorphic potential (49.5%) and broader molecular diversity (13-89%)/functional allelic diversity (18-77%) was apparent among 93 chickpea accessions, suggesting their tremendous applicability in rapid selection of desirable diverse accessions/inter-specific hybrids in chickpea crossbred varietal improvement program. The genome-wide SNPs revealed complex admixed domestication pattern, extensive LD estimates (0.54-0.68) and extended LD decay (400-500 kb) in a structured population inclusive of 93 accessions. These findings reflect the utility of our identified SNPs for subsequent genome-wide association study (GWAS) and selective sweep-based domestication trait dissection analysis to identify potential genomic loci (gene-associated targets) specifically regulating important complex quantitative agronomic traits in chickpea. The numerous informative genome-wide SNPs, natural allelic diversity-led domestication pattern, and LD-based information generated in our study have got multidimensional applicability with respect to chickpea genomics-assisted breeding.
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Affiliation(s)
- Alice Kujur
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Telangana, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Rajeev Ranjan
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Tanima Shree
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | | | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Vinod Kumar
- National Research Centre on Plant Biotechnology (NRCPB)New Delhi, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI)New Delhi, India
| | - C. L. L. Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Telangana, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Telangana, India
| | - Sube Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Telangana, India
| | | | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
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16
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CATS derived SNPs discovery in the golden snub-nosed monkey (Rhinopithecus roxellanae). CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-013-0005-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Cardoso DC, Martinati JC, Giachetto PF, Vidal RO, Carazzolle MF, Padilha L, Guerreiro-Filho O, Maluf MP. Large-scale analysis of differential gene expression in coffee genotypes resistant and susceptible to leaf miner-toward the identification of candidate genes for marker assisted-selection. BMC Genomics 2014; 15:66. [PMID: 24460833 PMCID: PMC3924705 DOI: 10.1186/1471-2164-15-66] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 01/13/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A successful development of herbivorous insects into plant tissues depends on coordination of metabolic processes. Plants have evolved complex mechanisms to recognize such attacks, and to trigger a defense response. To understand the transcriptional basis of this response, we compare gene expression profiles of two coffee genotypes, susceptible and resistant to leaf miner (Leucoptera coffella). A total of 22000 EST sequences from the Coffee Genome Database were selected for a microarray analysis. Fluorescence probes were synthesized using mRNA from the infested and non-infested coffee plants. Array hybridization, scanning and data normalization were performed using Nimble Scan® e ArrayStar® platforms. Genes with foldchange values +/-2 were considered differentially expressed. A validation of 18 differentially expressed genes was performed in infected plants using qRT-PCR approach. RESULTS The microarray analysis indicated that resistant plants differ in gene expression profile. We identified relevant transcriptional changes in defense strategies before insect attack. Expression changes (>2.00-fold) were found in resistant plants for 2137 genes (1266 up-regulated and 873 down-regulated). Up-regulated genes include those responsible for defense mechanisms, hypersensitive response and genes involved with cellular function and maintenance. Also, our analyses indicated that differential expression profiles between resistant and susceptible genotypes are observed in the absence of leaf-miner, indicating that defense is already build up in resistant plants, as a priming mechanism. Validation of selected genes pointed to four selected genes as suitable candidates for markers in assisted-selection of novel cultivars. CONCLUSIONS Our results show evidences that coffee defense responses against leaf-miner attack are balanced with other cellular functions. Also analyses suggest a major metabolic reconfiguration that highlights the complexity of this response.
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18
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Kuczenski RS, Aggarwal K, Lee KH. Improved understanding of gene expression regulation using systems biology. Expert Rev Proteomics 2014; 2:915-24. [PMID: 16307520 DOI: 10.1586/14789450.2.6.915] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This article reviews the current state of systems biology approaches, including the experimental tools used to generate 'omic' data and computational frameworks to interpret this data. Through illustrative examples, systems biology approaches to understand gene expression and gene expression regulation are discussed. Some of the challenges facing this field and the future opportunities in the systems biology era are highlighted.
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Affiliation(s)
- Robert S Kuczenski
- Cornell University, School of Chemical & Biomolecular Engineering, 120 Olin Hall, Ithaca, NY 14853, USA.
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19
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Sakurai T, Mochida K, Yoshida T, Akiyama K, Ishitani M, Seki M, Shinozaki K. Genome-wide discovery and information resource development of DNA polymorphisms in cassava. PLoS One 2013; 8:e74056. [PMID: 24040164 PMCID: PMC3770675 DOI: 10.1371/journal.pone.0074056] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/29/2013] [Indexed: 01/06/2023] Open
Abstract
Cassava (Manihot esculenta Crantz) is an important crop that provides food security and income generation in many tropical countries, and is known for its adaptability to various environmental conditions. Its draft genome sequence and many expressed sequence tags are now publicly available, allowing the development of cassava polymorphism information. Here, we describe the genome-wide discovery of cassava DNA polymorphisms. Using the alignment of predicted transcribed sequences from the cassava draft genome sequence and ESTs from GenBank, we discovered 10,546 single-nucleotide polymorphisms and 647 insertions and deletions. To facilitate molecular marker development for cassava, we designed 9,316 PCR primer pairs to amplify the genomic region around each DNA polymorphism. Of the discovered SNPs, 62.7% occurred in protein-coding regions. Disease-resistance genes were found to have a significantly higher ratio of nonsynonymous-to-synonymous substitutions. We identified 24 read-through (changes of a stop codon to a coding codon) and 38 premature stop (changes of a coding codon to a stop codon) single-nucleotide polymorphisms, and found that the 5 gene ontology terms in biological process were significantly different in genes with read-through single-nucleotide polymorphisms compared with all cassava genes. All data on the discovered DNA polymorphisms were organized into the Cassava Online Archive database, which is available at http://cassava.psc.riken.jp/.
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Affiliation(s)
- Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
- RIKEN Biomass Engineering Program, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Kanagawa, Japan
| | - Takuhiro Yoshida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Kenji Akiyama
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Manabu Ishitani
- Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Kanagawa, Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
- RIKEN Biomass Engineering Program, Tsurumi-ku, Yokohama, Kanagawa, Japan
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20
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Ren J, Sun D, Chen L, You FM, Wang J, Peng Y, Nevo E, Sun D, Luo MC, Peng J. Genetic diversity revealed by single nucleotide polymorphism markers in a worldwide germplasm collection of durum wheat. Int J Mol Sci 2013; 14:7061-88. [PMID: 23538839 PMCID: PMC3645677 DOI: 10.3390/ijms14047061] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 02/23/2013] [Accepted: 03/01/2013] [Indexed: 11/25/2022] Open
Abstract
Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity.
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Affiliation(s)
- Jing Ren
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan 430074, Hubei, China; E-Mails: (J.R.); (D.S.); (L.C.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daokun Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan 430074, Hubei, China; E-Mails: (J.R.); (D.S.); (L.C.)
| | - Liang Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan 430074, Hubei, China; E-Mails: (J.R.); (D.S.); (L.C.)
| | - Frank M. You
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; E-Mails: (F.M.Y.); (J.W.)
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, MB R3T 2M9, Canada
| | - Jirui Wang
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; E-Mails: (F.M.Y.); (J.W.)
| | - Yunliang Peng
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, Sichuan, China; E-Mail:
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel; E-Mail:
| | - Dongfa Sun
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430071, Hubei, China; E-Mail:
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; E-Mails: (F.M.Y.); (J.W.)
| | - Junhua Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan 430074, Hubei, China; E-Mails: (J.R.); (D.S.); (L.C.)
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
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21
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Ge AJ, Han J, Li XD, Zhao MZ, Liu H, Dong QH, Fang JG. Characterization of SNPs in strawberry cultivars in China. GENETICS AND MOLECULAR RESEARCH 2013; 12:639-45. [PMID: 23546945 DOI: 10.4238/2013.march.7.2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Single nucleotide polymorphisms (SNPs) occur at high frequencies in both plant and animal genomes and can provide broad genome coverage and reliable estimates of genetic relationships. The availability of expressed sequence tag (EST) data has made it feasible to discover SNPs. DNA analysis is crucial in genetic studies not only for strawberry breeding programs but also for characterization of hybrids and species. We cloned 96 EST sequences, and 116 SNPs were discovered by comparing 16 strawberry cultivars grown in the region of Nanjing, China. Sequence alignment of 6 group sequences derived from 16 sample cultivars yielded 116 SNPs, within a total genomic sequence length of 1755 bp. The SNPs were discovered with a mean frequency of one SNP per 15 bp. These SNPs were comprised of 57% transitions, 32.7% transversions, 8.6% InDels, and 1.7% others, based on which a phylogenetic tree was constructed. Among the 116 SNPs, 75% were located within the open reading frame (ORF), while 25% were located outside the ORF. All 16 cultivars scattered well in dendrogram derived from the SNP data, demonstrating that SNPs can be a powerful tool for cultivar identification and genetic diversity analysis in strawberries.
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Affiliation(s)
- A J Ge
- Beijing Key Laboratory of New Technology in Agricultural Application, Plant Science and Technology College, Beijing University of Agriculture, Beijing, P.R. China
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22
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Ward JA, Bhangoo J, Fernández-Fernández F, Moore P, Swanson JD, Viola R, Velasco R, Bassil N, Weber CA, Sargent DJ. Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genomics 2013. [PMID: 23324311 DOI: 10.1186/1471‐2164‐14‐2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry). Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker density, but result in some genotype errors and a large number of missing genotype values. Imputation can reduce the number of missing values and can correct genotyping errors, but current methods of imputation require a reference genome and thus are not an option for most species. RESULTS Genotyping by Sequencing (GBS) was used to produce highly saturated maps for a R. idaeus pseudo-testcross progeny. While low coverage and high variance in sequencing resulted in a large number of missing values for some individuals, a novel method of imputation based on maximum likelihood marker ordering from initial marker segregation overcame the challenge of missing values, and made map construction computationally tractable. The two resulting parental maps contained 4521 and 2391 molecular markers spanning 462.7 and 376.6 cM respectively over seven linkage groups. Detection of precise genomic regions with segregation distortion was possible because of map saturation. Microsatellites (SSRs) linked these results to published maps for cross-validation and map comparison. CONCLUSIONS GBS together with genome-independent imputation provides a rapid method for genetic map construction in any pseudo-testcross progeny. Our method of imputation estimates the correct genotype call of missing values and corrects genotyping errors that lead to inflated map size and reduced precision in marker placement. Comparison of SSRs to published R. idaeus maps showed that the linkage maps constructed with GBS and our method of imputation were robust, and marker positioning reliable. The high marker density allowed identification of genomic regions with segregation distortion in R. idaeus, which may help to identify deleterious alleles that are the basis of inbreeding depression in the species.
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Affiliation(s)
- Judson A Ward
- Department of Horticulture, Cornell University, New York State Agricultural Experiment Station, Geneva, New York 14456, USA.
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23
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Development of SNP markers associated with defense mechanism of sea cucumber, Apostichopus japonicas. CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-013-9858-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Ward JA, Bhangoo J, Fernández-Fernández F, Moore P, Swanson JD, Viola R, Velasco R, Bassil N, Weber CA, Sargent DJ. Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genomics 2013; 14:2. [PMID: 23324311 PMCID: PMC3575332 DOI: 10.1186/1471-2164-14-2] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 12/04/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry). Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker density, but result in some genotype errors and a large number of missing genotype values. Imputation can reduce the number of missing values and can correct genotyping errors, but current methods of imputation require a reference genome and thus are not an option for most species. RESULTS Genotyping by Sequencing (GBS) was used to produce highly saturated maps for a R. idaeus pseudo-testcross progeny. While low coverage and high variance in sequencing resulted in a large number of missing values for some individuals, a novel method of imputation based on maximum likelihood marker ordering from initial marker segregation overcame the challenge of missing values, and made map construction computationally tractable. The two resulting parental maps contained 4521 and 2391 molecular markers spanning 462.7 and 376.6 cM respectively over seven linkage groups. Detection of precise genomic regions with segregation distortion was possible because of map saturation. Microsatellites (SSRs) linked these results to published maps for cross-validation and map comparison. CONCLUSIONS GBS together with genome-independent imputation provides a rapid method for genetic map construction in any pseudo-testcross progeny. Our method of imputation estimates the correct genotype call of missing values and corrects genotyping errors that lead to inflated map size and reduced precision in marker placement. Comparison of SSRs to published R. idaeus maps showed that the linkage maps constructed with GBS and our method of imputation were robust, and marker positioning reliable. The high marker density allowed identification of genomic regions with segregation distortion in R. idaeus, which may help to identify deleterious alleles that are the basis of inbreeding depression in the species.
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Affiliation(s)
- Judson A Ward
- Department of Horticulture, Cornell University, New York State Agricultural Experiment Station, Geneva, New York 14456, USA.
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25
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Xu F, Feng S, Wu R, Du FK. Two highly validated SSR multiplexes (8-plex) for Euphrates' poplar, Populus euphratica (Salicaceae). Mol Ecol Resour 2012; 13:144-53. [PMID: 23134475 DOI: 10.1111/1755-0998.12030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 09/20/2012] [Accepted: 10/01/2012] [Indexed: 02/01/2023]
Abstract
Multiplex PCR amplification of microsatellites has significantly increased the throughput and decreased the costs of genotyping. We have developed two highly polymorphic microsatellite multiplexes for Populus euphratica, the only tree species found in desert regions of Western China and adjacent Central Asian countries. The first of these multiplex kits comprises an eight-Plex of genomic SSRs (gSSRs) obtained from published databases. The second comprises an eight-plex of newly designed EST-SSRs (eSSRs) based on expressed sequence tags for P. euphratica. Both kits were tested on a sample of 170 individuals from four populations. The gSSRs exhibited slightly more polymorphism than the eSSRs. The new multiplex protocols yielded consistent results in the hands of multiple researchers, demonstrating their robustness. The 16 loci used in the kits exhibited a high transferability rate (82.0%) in eight other poplar species belonging to five different sections of the genus. Both kits should therefore be useful for further investigations of population genetics in P. euphratica and related species. Our results indicate that it is essential to follow recently established recommendations when developing microsatellite markers, including verifying the amplification efficiency, detecting null alleles and carefully measuring error rates.
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Affiliation(s)
- Fang Xu
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
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de Miguel M, de Maria N, Guevara MA, Diaz L, Sáez-Laguna E, Sánchez-Gómez D, Chancerel E, Aranda I, Collada C, Plomion C, Cabezas JA, Cervera MT. Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers. BMC Genomics 2012; 13:527. [PMID: 23036012 PMCID: PMC3534022 DOI: 10.1186/1471-2164-13-527] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Accepted: 09/26/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. RESULTS We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. CONCLUSIONS This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.
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Affiliation(s)
- Marina de Miguel
- INIA-CIFOR, Departamento de Ecología y Genética Forestal, Madrid, Spain
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Van K, Kang YJ, Shim SR, Lee SH. Genome-wide scan of the soybean genome using degenerate oligonucleotide primed PCR: an example for studying large complex genome structure. Genes Genomics 2012. [DOI: 10.1007/s13258-011-0238-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Du H, Bao Z, Yan J, Tian M, Mu X, Wang S, Lu W. Development of 101 gene-based single nucleotide polymorphism markers in sea cucumber, Apostichopus japonicus. Int J Mol Sci 2012; 13:7080-7097. [PMID: 22837680 PMCID: PMC3397512 DOI: 10.3390/ijms13067080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 05/25/2012] [Accepted: 05/25/2012] [Indexed: 11/21/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are currently the marker of choice in a variety of genetic studies. Using the high resolution melting (HRM) genotyping approach, 101 gene-based SNP markers were developed for Apostichopus japonicus, a sea cucumber species with economic significance for the aquaculture industry in East Asian countries. HRM analysis revealed that all the loci showed polymorphisms when evaluated using 40 A. japonicus individuals collected from a natural population. The minor allele frequency ranged from 0.035 to 0.489. The observed and expected heterozygosities ranged from 0.050 to 0.833 and 0.073 to 0.907, respectively. Thirteen loci were found to depart significantly from Hardy-Weinberg equilibrium (HWE) after Bonferroni corrections. Significant linkage disequilibrium (LD) was detected in one pair of markers. These SNP markers are expected to be useful for future quantitative trait loci (QTL) analysis, and to facilitate marker-assisted selection (MAS) in A. japonicus.
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Affiliation(s)
- Huixia Du
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China; E-Mails: (H.D.); (Z.B.); (J.Y.); (M.T.); (X.M.); (S.W.)
| | - Zhenmin Bao
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China; E-Mails: (H.D.); (Z.B.); (J.Y.); (M.T.); (X.M.); (S.W.)
| | - Jingjing Yan
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China; E-Mails: (H.D.); (Z.B.); (J.Y.); (M.T.); (X.M.); (S.W.)
| | - Meilin Tian
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China; E-Mails: (H.D.); (Z.B.); (J.Y.); (M.T.); (X.M.); (S.W.)
| | - Xiaoyu Mu
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China; E-Mails: (H.D.); (Z.B.); (J.Y.); (M.T.); (X.M.); (S.W.)
| | - Shi Wang
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China; E-Mails: (H.D.); (Z.B.); (J.Y.); (M.T.); (X.M.); (S.W.)
| | - Wei Lu
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China; E-Mails: (H.D.); (Z.B.); (J.Y.); (M.T.); (X.M.); (S.W.)
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Analysis of genetic mapping in a waxy/dent maize RIL population using SSR and SNP markers. Genes Genomics 2012. [DOI: 10.1007/s13258-011-0208-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ferguson ME, Hearne SJ, Close TJ, Wanamaker S, Moskal WA, Town CD, de Young J, Marri PR, Rabbi IY, de Villiers EP. Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:685-95. [PMID: 22069119 DOI: 10.1007/s00122-011-1739-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 10/18/2011] [Indexed: 05/05/2023]
Abstract
The availability of genomic resources can facilitate progress in plant breeding through the application of advanced molecular technologies for crop improvement. This is particularly important in the case of less researched crops such as cassava, a staple and food security crop for more than 800 million people. Here, expressed sequence tags (ESTs) were generated from five drought stressed and well-watered cassava varieties. Two cDNA libraries were developed: one from root tissue (CASR), the other from leaf, stem and stem meristem tissue (CASL). Sequencing generated 706 contigs and 3,430 singletons. These sequences were combined with those from two other EST sequencing initiatives and filtered based on the sequence quality. Quality sequences were aligned using CAP3 and embedded in a Windows browser called HarvEST:Cassava which is made available. HarvEST:Cassava consists of a Unigene set of 22,903 quality sequences. A total of 2,954 putative SNPs were identified. Of these 1,536 SNPs from 1,170 contigs and 53 cassava genotypes were selected for SNP validation using Illumina's GoldenGate assay. As a result 1,190 SNPs were validated technically and biologically. The location of validated SNPs on scaffolds of the cassava genome sequence (v.4.1) is provided. A diversity assessment of 53 cassava varieties reveals some sub-structure based on the geographical origin, greater diversity in the Americas as opposed to Africa, and similar levels of diversity in West Africa and southern, eastern and central Africa. The resources presented allow for improved genetic dissection of economically important traits and the application of modern genomics-based approaches to cassava breeding and conservation.
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Affiliation(s)
- Morag E Ferguson
- International Institute of Tropical Agriculture (IITA), c/o ILRI, P.O. Box 30709, Nairobi, Kenya.
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Allegre M, Argout X, Boccara M, Fouet O, Roguet Y, Bérard A, Thévenin JM, Chauveau A, Rivallan R, Clement D, Courtois B, Gramacho K, Boland-Augé A, Tahi M, Umaharan P, Brunel D, Lanaud C. Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L. DNA Res 2011; 19:23-35. [PMID: 22210604 PMCID: PMC3276266 DOI: 10.1093/dnares/dsr039] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high-density genetic map. By screening 149 650 ESTs, 5246 SNPs were detected in silico, of which 1536 corresponded to genes with a putative function, while 851 had a clear polymorphic pattern across a collection of genetic resources. In addition, 409 new SSR markers were detected on the Criollo genome. Lastly, 681 new EST-SNPs and 163 new SSRs were added to the pre-existing 418 co-dominant markers to construct a large consensus genetic map. This high-density map and the set of new genetic markers identified in this study are a milestone in cocoa genomics and for marker-assisted breeding. The data are available at http://tropgenedb.cirad.fr.
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Affiliation(s)
- Mathilde Allegre
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
| | - Xavier Argout
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
- To whom correspondence should be addressed. Fax. +33 4-67-61-56-05.
| | - Michel Boccara
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
- University of the West Indies, Cocoa Research Unit (CRU), St Augustine, Trinidad and Tobago
| | - Olivier Fouet
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
| | - Yolande Roguet
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
| | - Aurélie Bérard
- INRA, UR 1279 Etude du Polymorphisme des Génomes Végétaux, CEA Institut de Génomique, Centre National de Génotypage, 2, rue Gaston Crémieux, CP5724, 91057 Evry, France
| | - Jean Marc Thévenin
- CIRAD, Biological Systems Department, UPR Bioagresseurs, 97387 Kourou Cedex, French Guiana
| | - Aurélie Chauveau
- INRA, UR 1279 Etude du Polymorphisme des Génomes Végétaux, CEA Institut de Génomique, Centre National de Génotypage, 2, rue Gaston Crémieux, CP5724, 91057 Evry, France
| | - Ronan Rivallan
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
| | - Didier Clement
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
- Comissão Executiva de Planejamento da Lavoura Cacaueira (CEPLAC), Km 22 Rod. Ilheus Itabuna, Cx. postal 07, Itabuna 45600-00, Bahia, Brazil
| | | | - Karina Gramacho
- Comissão Executiva de Planejamento da Lavoura Cacaueira (CEPLAC), Km 22 Rod. Ilheus Itabuna, Cx. postal 07, Itabuna 45600-00, Bahia, Brazil
| | - Anne Boland-Augé
- INRA, UR 1279 Etude du Polymorphisme des Génomes Végétaux, CEA Institut de Génomique, Centre National de Génotypage, 2, rue Gaston Crémieux, CP5724, 91057 Evry, France
| | - Mathias Tahi
- Centre National de la Recherche Agronomique (CNRA), B.P. 808, Divo, Côte d'Ivoire
| | - Pathmanathan Umaharan
- University of the West Indies, Cocoa Research Unit (CRU), St Augustine, Trinidad and Tobago
| | - Dominique Brunel
- INRA, UR 1279 Etude du Polymorphisme des Génomes Végétaux, CEA Institut de Génomique, Centre National de Génotypage, 2, rue Gaston Crémieux, CP5724, 91057 Evry, France
| | - Claire Lanaud
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
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Weckwerth W. Green systems biology - From single genomes, proteomes and metabolomes to ecosystems research and biotechnology. J Proteomics 2011; 75:284-305. [PMID: 21802534 DOI: 10.1016/j.jprot.2011.07.010] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 07/07/2011] [Accepted: 07/10/2011] [Indexed: 12/13/2022]
Abstract
Plants have shaped our human life form from the outset. With the emerging recognition of world population feeding, global climate change and limited energy resources with fossil fuels, the relevance of plant biology and biotechnology is becoming dramatically important. One key issue is to improve plant productivity and abiotic/biotic stress resistance in agriculture due to restricted land area and increasing environmental pressures. Another aspect is the development of CO(2)-neutral plant resources for fiber/biomass and biofuels: a transition from first generation plants like sugar cane, maize and other important nutritional crops to second and third generation energy crops such as Miscanthus and trees for lignocellulose and algae for biomass and feed, hydrogen and lipid production. At the same time we have to conserve and protect natural diversity and species richness as a foundation of our life on earth. Here, biodiversity banks are discussed as a foundation of current and future plant breeding research. Consequently, it can be anticipated that plant biology and ecology will have more indispensable future roles in all socio-economic aspects of our life than ever before. We therefore need an in-depth understanding of the physiology of single plant species for practical applications as well as the translation of this knowledge into complex natural as well as anthropogenic ecosystems. Latest developments in biological and bioanalytical research will lead into a paradigm shift towards trying to understand organisms at a systems level and in their ecosystemic context: (i) shotgun and next-generation genome sequencing, gene reconstruction and annotation, (ii) genome-scale molecular analysis using OMICS technologies and (iii) computer-assisted analysis, modeling and interpretation of biological data. Systems biology combines these molecular data, genetic evolution, environmental cues and species interaction with the understanding, modeling and prediction of active biochemical networks up to whole species populations. This process relies on the development of new technologies for the analysis of molecular data, especially genomics, metabolomics and proteomics data. The ambitious aim of these non-targeted 'omic' technologies is to extend our understanding beyond the analysis of separated parts of the system, in contrast to traditional reductionistic hypothesis-driven approaches. The consequent integration of genotyping, pheno/morphotyping and the analysis of the molecular phenotype using metabolomics, proteomics and transcriptomics will reveal a novel understanding of plant metabolism and its interaction with the environment. The analysis of single model systems - plants, fungi, animals and bacteria - will finally emerge in the analysis of populations of plants and other organisms and their adaptation to the ecological niche. In parallel, this novel understanding of ecophysiology will translate into knowledge-based approaches in crop plant biotechnology and marker- or genome-assisted breeding approaches. In this review the foundations of green systems biology are described and applications in ecosystems research are presented. Knowledge exchange of ecosystems research and green biotechnology merging into green systems biology is anticipated based on the principles of natural variation, biodiversity and the genotype-phenotype environment relationship as the fundamental drivers of ecology and evolution.
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Affiliation(s)
- Wolfram Weckwerth
- Department of Molecular Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
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Babu R, Jiang CJ, Xu X, Kottapalli KR, Takatsuji H, Miyao A, Hirochika H, Kawasaki S. Isolation, fine mapping and expression profiling of a lesion mimic genotype, spl(NF4050-8) that confers blast resistance in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:831-854. [PMID: 21132425 DOI: 10.1007/s00122-010-1490-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 11/04/2010] [Indexed: 05/30/2023]
Abstract
We evaluated a large collection of Tos17 mutant panel lines for their reaction to three different races of Magnaporthe oryzae and identified a lesion mimic mutant, NF4050-8, that showed lesions similar to naturally occurring spl5 mutant and enhanced resistance to all the three blast races tested. Nested modified-AFLP using Tos17-specific primers and southern hybridization experiments of segregating individuals indicated that the lesion mimic phenotype in NF4050-8 is most likely due to a nucleotide change acquired during the culturing process and not due to Tos17 insertion per se. Inheritance and genetic analyses in two japonica × indica populations identified an overlapping genomic region of 13 cM on short arm of chromosome 7 that was linked with the lesion mimic phenotype. High-resolution genetic mapping using 950 F(3) and 3,821 F(4) plants of NF4050-8 × CO39 delimited a 35 kb region flanked by NBARC1 (5.262 Mb) and RM8262 (5.297 Mb), which contained 6 ORFs; 3 of them were 'resistance gene related' with typical NBS-LRR signatures. One of them harbored a NB-ARC domain, which had been previously demonstrated to be associated with cell death in animals. Microarray analysis of NF4050-8 revealed significant up-regulation of numerous defense/pathogenesis-related genes and down-regulation of heme peroxidase genes. Real-time PCR analysis of WRKY45 and PR1b genes suggested possible constitutive activation of a defense signaling pathway downstream of salicylic acid but independent of NH1 in these mutant lines of rice.
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Affiliation(s)
- Raman Babu
- National Institute of Agrobiosciences (NIAS), Tsukuba, Ibaraki, Japan.
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Hirotsu N, Murakami N, Kashiwagi T, Ujiie K, Ishimaru K. Protocol: a simple gel-free method for SNP genotyping using allele-specific primers in rice and other plant species. PLANT METHODS 2010; 6:12. [PMID: 20409329 PMCID: PMC2876155 DOI: 10.1186/1746-4811-6-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 04/21/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND Genotype analysis using multiple single nucleotide polymorphisms (SNPs) is a useful but labor-intensive or high-cost procedure in plant research. Here we describe an alternative genotyping method that is suited to multi-sample or multi-locus SNP genotyping and does not require electrophoresis or specialized equipment. RESULTS We have developed a simple method for multi-sample or multi-locus SNP genotyping using allele-specific primers (ASP). More specifically, we (1) improved the design of allele-specific primers, (2) established a method to detect PCR products optically without electrophoresis, and (3) standardized PCR conditions for parallel genomic assay using various allele-specific primers. As an illustration of multi-sample SNP genotyping using ASP, we mapped the locus for lodging resistance in a typhoon (lrt5). Additionally, we successfully tested multi-locus ASP-PCR analysis using 96 SNPs located throughout the genomes of rice (Oryza sativa) cultivars 'Koshihikari' and 'Kasalath', and demonstrated its applicability to other diverse cultivars/subspecies, including wild rice (O. rufipogon). CONCLUSION Our ASP methodology allows characterization of SNPs genotypes without electrophoresis, expensive probes or specialized equipment, and is highly versatile due to the flexibility in the design of primers. The method could be established easily in any molecular biology laboratory, and is applicable to diverse organisms.
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Affiliation(s)
- Naoki Hirotsu
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
- Current address: Department of Life Sciences, Faculty of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Gunma 374-0193, Japan
| | - Naomi Murakami
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Takayuki Kashiwagi
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
- Current address: Department of Bioproductive Science, Faculty of Agriculture, Utsunomiya University, 350 Mine, Utsunomiya, Tochigi 321-8505, Japan
| | - Kazuhiro Ujiie
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Ken Ishimaru
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
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Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ. Target-enrichment strategies for next-generation sequencing. Nat Methods 2010; 7:111-8. [PMID: 20111037 DOI: 10.1038/nmeth.1419] [Citation(s) in RCA: 761] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have not yet reached a point at which routine sequencing of large numbers of whole eukaryotic genomes is feasible, and so it is often necessary to select genomic regions of interest and to enrich these regions before sequencing. There are several enrichment approaches, each with unique advantages and disadvantages. Here we describe our experiences with the leading target-enrichment technologies, the optimizations that we have performed and typical results that can be obtained using each. We also provide detailed protocols for each technology so that end users can find the best compromise between sensitivity, specificity and uniformity for their particular project.
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Affiliation(s)
- Lira Mamanova
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Stich B, Utz HF, Piepho HP, Maurer HP, Melchinger AE. Optimum allocation of resources for QTL detection using a nested association mapping strategy in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:553-561. [PMID: 19847390 PMCID: PMC2807940 DOI: 10.1007/s00122-009-1175-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 09/30/2009] [Indexed: 05/28/2023]
Abstract
In quantitative trait locus (QTL) mapping studies, it is mandatory that the available financial resources are spent in such a way that the power for detection of QTL is maximized. The objective of this study was to optimize for three different fixed budgets the power of QTL detection 1 - beta* in recombinant inbred line (RIL) populations derived from a nested design by varying (1) the genetic complexity of the trait, (2) the costs for developing, genotyping, and phenotyping RILs, (3) the total number of RILs, and (4) the number of environments and replications per environment used for phenotyping. Our computer simulations were based on empirical data of 653 single nucleotide polymorphism markers of 26 diverse maize inbred lines which were selected on the basis of 100 simple sequence repeat markers out of a worldwide sample of 260 maize inbreds to capture the maximum genetic diversity. For the standard scenario of costs, the optimum number of test environments (E (opt)) ranged across the examined total budgets from 7 to 19 in the scenarios with 25 QTL. In comparison, the E (opt) values observed for the scenarios with 50 and 100 QTL were slightly higher. Our finding of differences in 1 - beta* estimates between experiments with optimally and sub-optimally allocated resources illustrated the potential to improve the power for QTL detection without increasing the total resources necessary for a QTL mapping experiment. Furthermore, the results of our study indicated that also in studies using the latest genomics tools to dissect quantitative traits, it is required to evaluate the individuals of the mapping population in a high number of environments with a high number of replications per environment.
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Affiliation(s)
- Benjamin Stich
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
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Cao WB, Zheng LL, Zhang ZF, Li XB. Genetic diversity of starch synthesis genes of Chinese maize (Zea mays L.) with SNAPs. Mol Biol 2009. [DOI: 10.1134/s0026893309060041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Guerra Cardoso H, Doroteia Campos M, Rita Costa A, Catarina Campos M, Nothnagel T, Arnholdt-Schmitt B. Carrot alternative oxidase gene AOX2a demonstrates allelic and genotypic polymorphisms in intron 3. PHYSIOLOGIA PLANTARUM 2009; 137:592-608. [PMID: 19941625 DOI: 10.1111/j.1399-3054.2009.01299.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) are becoming important genetic markers for major crop species. In this study, we focus on variations at genomic level of the Daucus carota L. AOX2a gene. The use of gene-specific primers designed in exon regions on the boundaries of introns permitted to recognize intron length polymorphism (ILP) in intron 3 AOX2a by simple polymerase chain reaction (PCR) assays. The length of intron 3 can vary in individual carrot plants. Thus, allelic variation can be used as a tool to discriminate between single plant genotypes. Using this approach, individual plants from cv. Rotin and from diverse breeding lines and cultivars were identified that showed genetic variability by AOX2a ILPs. Repetitive patterns of intron length variation have been observed which allows grouping of genotypes. Polymorphic and identical PCR fragments revealed underlying high levels of sequence polymorphism. Variability was due to InDel events and intron single nucleotide polymorphisms (ISNPs), with a repetitive deletion in intron 3 affecting a putative pre-miRNA site. The results suggest that high AOX2a gene diversity in D. carota can be explored for the development of functional markers related to agronomic traits.
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Affiliation(s)
- Hélia Guerra Cardoso
- EU Marie Curie Chair, ICAAM, University of Evora, Apartado 94, 7002-554 Evora, Portugal
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Papdi C, Joseph MP, Salamó IP, Vidal S, Szabados L. Genetic technologies for the identification of plant genes controlling environmental stress responses. FUNCTIONAL PLANT BIOLOGY : FPB 2009; 36:696-720. [PMID: 32688681 DOI: 10.1071/fp09047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 06/11/2009] [Indexed: 06/11/2023]
Abstract
Abiotic conditions such as light, temperature, water availability and soil parameters determine plant growth and development. The adaptation of plants to extreme environments or to sudden changes in their growth conditions is controlled by a well balanced, genetically determined signalling system, which is still far from being understood. The identification and characterisation of plant genes which control responses to environmental stresses is an essential step to elucidate the complex regulatory network, which determines stress tolerance. Here, we review the genetic approaches, which have been used with success to identify plant genes which control responses to different abiotic stress factors. We describe strategies and concepts for forward and reverse genetic screens, conventional and insertion mutagenesis, TILLING, gene tagging, promoter trapping, activation mutagenesis and cDNA library transfer. The utility of the various genetic approaches in plant stress research we review is illustrated by several published examples.
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Affiliation(s)
- Csaba Papdi
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Mary Prathiba Joseph
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Imma Pérez Salamó
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Sabina Vidal
- Facultad de Ciencias, Universidad de la República, Iguá 4225, CP 11400, Montevideo, Uruguay
| | - László Szabados
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
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A comprehensive assay for targeted multiplex amplification of human DNA sequences. Proc Natl Acad Sci U S A 2008; 105:9296-301. [PMID: 18599465 DOI: 10.1073/pnas.0803240105] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We developed a robust and reproducible methodology to amplify human sequences in parallel for use in downstream multiplexed sequence analyses. We call the methodology SMART (Spacer Multiplex Amplification Reaction), and it is based, in part, on padlock probe technology. As a proof of principle, we used SMART technology to simultaneously amplify 485 human exons ranging from 100 to 500 bp from human genomic DNA. In multiple repetitions, >90% of the targets were successfully amplified with a high degree of uniformity, with 70% of targets falling within a 10-fold range and all products falling within a 100-fold range of each other in abundance. We used long padlock probes (LPPs) >300 bases in length for the assay, and the increased length of these probes allowed for the capture of human sequences up to 500 bp in length, which is optimal for capturing most human exons. To engineer the LPPs, we developed a method that generates ssDNA molecules with precise ends, using an appropriately designed dsDNA template. The template has appropriate restriction sites engineered into it that can be digested to generate nucleotide overhangs that are suitable for lambda exonuclease digestion, producing a single-stranded probe from dsDNA. The SMART technology is flexible and can be easily adapted to multiplex tens of thousands of target sequences in a single reaction.
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Rapid bio-barcode assay for multiplex DNA detection based on capillary DNA Analyzer. J Virol Methods 2008; 151:126-31. [DOI: 10.1016/j.jviromet.2008.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 02/24/2008] [Accepted: 03/04/2008] [Indexed: 11/18/2022]
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Gupta PK, Rustgi S, Mir RR. Array-based high-throughput DNA markers for crop improvement. Heredity (Edinb) 2008; 101:5-18. [PMID: 18461083 DOI: 10.1038/hdy.2008.35] [Citation(s) in RCA: 242] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The last two decades have witnessed a remarkable activity in the development and use of molecular markers both in animal and plant systems. This activity started with low-throughput restriction fragment length polymorphisms and culminated in recent years with single nucleotide polymorphisms (SNPs), which are abundant and uniformly distributed. Although the latter became the markers of choice for many, their discovery needed previous sequence information. However, with the availability of microarrays, SNP platforms have been developed, which allow genotyping of thousands of markers in parallel. Besides SNPs, some other novel marker systems, including single feature polymorphisms, diversity array technology and restriction site-associated DNA markers, have also been developed, where array-based assays have been utilized to provide for the desired ultra-high throughput and low cost. These microarray-based markers are the markers of choice for the future and are already being used for construction of high-density maps, quantitative trait loci (QTL) mapping (including expression QTLs) and genetic diversity analysis with a limited expense in terms of time and money. In this study, we briefly describe the characteristics of these array-based marker systems and review the work that has already been done involving development and use of these markers, not only in simple eukaryotes like yeast, but also in a variety of seed plants with simple or complex genomes.
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Affiliation(s)
- P K Gupta
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, Uttar Pradesh, India.
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An C, Saha S, Jenkins JN, Ma DP, Scheffler BE, Kohel RJ, Yu JZ, Stelly DM. Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylogenomic characterization, chromosome localization, and linkage mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:1015-26. [PMID: 18338155 DOI: 10.1007/s00122-008-0732-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Accepted: 02/11/2008] [Indexed: 05/08/2023]
Abstract
R2R3-MYB transcription factors of plants are involved in the regulation of trichome length and density. Several of them are differentially expressed during initiation and elongation of cotton fibers. We report sequence phylogenomic characterization of the six MYB genes, their chromosomal localization, and linkage mapping via SNP marker in AD-genome cotton (2n = 52). Phylogenetic grouping and comparison to At- and Dt-genome putative ancestral diploid species of allotetraploid cotton facilitated differentiation between genome-specific polymorphisms (GSPs) and marker-suitable locus-specific polymorphisms (LSPs). The SNP frequency averaged one per 77 bases overall, and one per 106 and 30 bases in coding and non-coding regions, respectively. SNP-based multivariate relationships conformed to independent evolution of the six MYB homoeologous loci in the four tetraploid species. Nucleotide diversity analysis indicated that the six MYB loci evolved more quickly in the Dt- than At-genome. The greater variation in the Dt-D genome comparisons than that in At-A genome comparisons showed no significant bias among synonymous substitution, non-synonymous substitution, and nucleotide change in non-coding regions. SNPs were concordantly mapped by deletion analysis and linkage mapping, which confirmed their value as candidate gene markers and indicated the reliability of the SNP discovery strategy in tetraploid cotton species. We consider that these SNPs may be useful for genetic dissection of economically important fiber and yield traits because of the role of these genes in fiber development.
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Affiliation(s)
- Chuanfu An
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA
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Chen D, Ahlford A, Schnorrer F, Kalchhauser I, Fellner M, Viràgh E, Kiss I, Syvänen AC, Dickson BJ. High-resolution, high-throughput SNP mapping in Drosophila melanogaster. Nat Methods 2008; 5:323-9. [DOI: 10.1038/nmeth.1191] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Accepted: 02/13/2008] [Indexed: 11/10/2022]
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Törjék O, Meyer RC, Zehnsdorf M, Teltow M, Strompen G, Witucka-Wall H, Blacha A, Altmann T. Construction and analysis of 2 reciprocal Arabidopsis introgression line populations. ACTA ACUST UNITED AC 2008; 99:396-406. [PMID: 18310067 DOI: 10.1093/jhered/esn014] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Two new large reciprocal sets of introgression lines (ILs) were created between the Arabidopsis accessions Col-0 and C24. In both sets (78 ILs with Col-0 background and 62 ILs with C24 background), the donor segments cover almost the entire genome with an average substitution size of 18.3 cM. In addition to the basic sets of ILs, further subILs were developed for 2 genomic regions allowing better mapping resolution. SubILs carrying donor segments with candidate genes for flowering time and reduced fertility were used to demonstrate the usefulness of the reciprocal ILs for quantitative trait loci detection and fine mapping. For subIL development at high resolution around the reduced fertility locus, we used modified CelI-based assays in one-well format for both marker development and genotyping. This serves as a very flexible and cost-effective approach.
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Affiliation(s)
- Ottó Törjék
- Department of Genetics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
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Fusari CM, Lia VV, Hopp HE, Heinz RA, Paniego NB. Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach. BMC PLANT BIOLOGY 2008; 8:7. [PMID: 18215288 PMCID: PMC2266750 DOI: 10.1186/1471-2229-8-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 01/23/2008] [Indexed: 05/04/2023]
Abstract
BACKGROUND Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD) and the evaluation of selection processes. Trait mapping by allele association requires a high-density map, which could be obtained by the addition of Single Nucleotide Polymorphisms (SNPs) and short insertion and/or deletions (indels) to SSR and AFLP genetic maps. Nucleotide diversity analysis of randomly selected candidate regions is a promising approach for the success of association analysis and fine mapping in the sunflower genome. Moreover, knowledge of the distance over which LD persists, in agronomically meaningful sunflower accessions, is important to establish the density of markers and the experimental design for association analysis. RESULTS A set of 28 candidate genes related to biotic and abiotic stresses were studied in 19 sunflower inbred lines. A total of 14,348 bp of sequence alignment was analyzed per individual. In average, 1 SNP was found per 69 nucleotides and 38 indels were identified in the complete data set. The mean nucleotide polymorphism was moderate (theta = 0.0056), as expected for inbred materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 +/- 1.88). Model-based population structure analysis allowed detection of admixed individuals within the set of accessions examined. Two putative gene pools were identified (G1 and G2), with a large proportion of the inbred lines being assigned to one of them (G1). Consistent with the absence of population sub-structuring, LD for G1 decayed more rapidly (r2 = 0.48 at 643 bp; trend line, pooled data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance). CONCLUSION Knowledge about the patterns of diversity and the genetic relationships between breeding materials could be an invaluable aid in crop improvement strategies. The relatively high frequency of SNPs within the elite inbred lines studied here, along with the predicted extent of LD over distances of 100 kbp (r2 approximately 0.1) suggest that high resolution association mapping in sunflower could be achieved with marker densities lower than those usually reported in the literature.
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Affiliation(s)
- Corina M Fusari
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
| | - Verónica V Lia
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - H Esteban Hopp
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ruth A Heinz
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Norma B Paniego
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
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Fusari CM, Lia VV, Hopp HE, Heinz RA, Paniego NB. Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach. BMC PLANT BIOLOGY 2008; 8:7. [PMID: 18215288 DOI: 10.1186/147-2229.8-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 01/23/2008] [Indexed: 05/20/2023]
Abstract
BACKGROUND Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD) and the evaluation of selection processes. Trait mapping by allele association requires a high-density map, which could be obtained by the addition of Single Nucleotide Polymorphisms (SNPs) and short insertion and/or deletions (indels) to SSR and AFLP genetic maps. Nucleotide diversity analysis of randomly selected candidate regions is a promising approach for the success of association analysis and fine mapping in the sunflower genome. Moreover, knowledge of the distance over which LD persists, in agronomically meaningful sunflower accessions, is important to establish the density of markers and the experimental design for association analysis. RESULTS A set of 28 candidate genes related to biotic and abiotic stresses were studied in 19 sunflower inbred lines. A total of 14,348 bp of sequence alignment was analyzed per individual. In average, 1 SNP was found per 69 nucleotides and 38 indels were identified in the complete data set. The mean nucleotide polymorphism was moderate (theta = 0.0056), as expected for inbred materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 +/- 1.88). Model-based population structure analysis allowed detection of admixed individuals within the set of accessions examined. Two putative gene pools were identified (G1 and G2), with a large proportion of the inbred lines being assigned to one of them (G1). Consistent with the absence of population sub-structuring, LD for G1 decayed more rapidly (r2 = 0.48 at 643 bp; trend line, pooled data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance). CONCLUSION Knowledge about the patterns of diversity and the genetic relationships between breeding materials could be an invaluable aid in crop improvement strategies. The relatively high frequency of SNPs within the elite inbred lines studied here, along with the predicted extent of LD over distances of 100 kbp (r2 approximately 0.1) suggest that high resolution association mapping in sunflower could be achieved with marker densities lower than those usually reported in the literature.
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Affiliation(s)
- Corina M Fusari
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina.
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Van K, Onoda S, Kim MY, Kim KD, Lee SH. Allelic variation of the Waxy gene in foxtail millet [Setaria italica (L.) P. Beauv.] by single nucleotide polymorphisms. Mol Genet Genomics 2007; 279:255-66. [PMID: 18157676 DOI: 10.1007/s00438-007-0310-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Accepted: 11/28/2007] [Indexed: 11/29/2022]
Abstract
The Waxy (Wx) gene product controls the formation of a straight chain polymer of amylose in the starch pathway. Dominance/recessiveness of the Wx allele is associated with amylose content, leading to non-waxy/waxy phenotypes. For a total of 113 foxtail millet accessions, agronomic traits and the molecular differences of the Wx gene were surveyed to evaluate genetic diversities. Molecular types were associated with phenotypes determined by four specific primer sets (non-waxy, Type I; low amylose, Type VI; waxy, Type IV or V). Additionally, the insertion of transposable element in waxy was confirmed by ex1/TSI2R, TSI2F/ex2, ex2int2/TSI7R and TSI7F/ex4r. Seventeen single nucleotide polymorphims (SNPs) were observed from non-coding regions, while three SNPs from coding regions were non-synonymous. Interestingly, the phenotype of No. 88 was still non-waxy, although seven nucleotides (AATTGGT) insertion at 2,993 bp led to 78 amino acids shorter. The rapid decline of r (2) in the sequenced region (exon 1-intron 1-exon 2) suggested a low level of linkage disequilibrium and limited haplotype structure. K (s) values and estimation of evolutionary events indicate early divergence of S. italica among cereal crops. This study suggested the Wx gene was one of the targets in the selection process during domestication.
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Affiliation(s)
- K Van
- Department of Plant Science, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul, 151-921, The Republic of Korea
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Sauvage C, Bierne N, Lapègue S, Boudry P. Single Nucleotide polymorphisms and their relationship to codon usage bias in the Pacific oyster Crassostrea gigas. Gene 2007; 406:13-22. [PMID: 17616269 DOI: 10.1016/j.gene.2007.05.011] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 05/14/2007] [Accepted: 05/18/2007] [Indexed: 10/23/2022]
Abstract
DNA sequence polymorphism and codon usage bias were investigated in a set of 41 nuclear loci in the Pacific oyster Crassostrea gigas. Our results revealed a very high level of DNA polymorphism in oysters, in the order of magnitude of the highest levels reported in animals to date. A total of 290 single nucleotide polymorphisms (SNPs) were detected, 76 of which being localised in exons and 214 in non-coding regions. Average density of SNPs was estimated to be one SNP every 60 bp in coding regions and one every 40 bp in non-coding regions. Non-synonymous substitutions contributed substantially to the polymorphism observed in coding regions. The non-synonymous to silent diversity ratio was 0.16 on average, which is fairly higher to the ratio reported in other invertebrate species recognised to display large population sizes. Therefore, purifying selection does not appear to be as strong as it could have been expected for a species with a large effective population size. The level of non-synonymous diversity varied greatly from one gene to another, in accordance with varying selective constraints. We examined codon usage bias and its relationship with DNA polymorphism. The table of optimal codons was deduced from the analysis of an EST dataset, using EST counts as a rough assessment of gene expression. As recently observed in some other taxa, we found a strong and significant negative relationship between codon bias and non-synonymous diversity suggesting correlated selective constraints on synonymous and non-synonymous substitutions. Codon bias as measured by the frequency of optimal codons for expression might therefore provide a useful indicator of the level of constraint upon proteins in the oyster genome.
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Affiliation(s)
- C Sauvage
- Laboratoire de Génétique et Pathologie - IFREMER - La Tremblade, France
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Hamzeh M, Sawchyn C, Périnet P, Dayanandan S. Asymmetrical natural hybridization betweenPopulus deltoidesandP.balsamifera(Salicaceae)This note is one of a selection of papers published in the Special Issue on Poplar Research in Canada. ACTA ACUST UNITED AC 2007. [DOI: 10.1139/b07-105] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Natural hybridization has long been recognized as a means for gene flow between species and has important evolutionary consequences. Although hybridization is generally considered to be symmetrical, with both hybridizing species being equally likely to be the male or female parent, several studies have demonstrated the presence of asymmetrical hybridization and introgression from one species to the other. We investigated the direction of natural hybridization between two sympatric forest tree species in North America ( Populus deltoides Bartr. ex Marsh. and Populus balsamifera L.) using species-specific single nucleotide polymorphism (SNP) markers in both the nuclear and chloroplast genomes. All natural hybrid individuals, identified from morphological traits, had nuclear alleles corresponding to both parental species, while the chloroplast genotypes showed similarity to P. deltoides, indicating asymmetrical hybridization with P. deltoides as the maternal and P. balsamifera as the paternal donor species. This observed asymmetrical hybridization may be attributable to cytonuclear interactions.
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Affiliation(s)
- Mona Hamzeh
- Biology Department, Concordia University, 7141 Sherbrooke St. West, Montreal, QC H4B 1R6, Canada
- Direction de la recherche forestière, Ministère des Ressources naturelles et de la Faune, 2700, rue Einstein, Sainte-Foy, QC G1P 3W8, Canada
| | - Christina Sawchyn
- Biology Department, Concordia University, 7141 Sherbrooke St. West, Montreal, QC H4B 1R6, Canada
- Direction de la recherche forestière, Ministère des Ressources naturelles et de la Faune, 2700, rue Einstein, Sainte-Foy, QC G1P 3W8, Canada
| | - Pierre Périnet
- Biology Department, Concordia University, 7141 Sherbrooke St. West, Montreal, QC H4B 1R6, Canada
- Direction de la recherche forestière, Ministère des Ressources naturelles et de la Faune, 2700, rue Einstein, Sainte-Foy, QC G1P 3W8, Canada
| | - Selvadurai Dayanandan
- Biology Department, Concordia University, 7141 Sherbrooke St. West, Montreal, QC H4B 1R6, Canada
- Direction de la recherche forestière, Ministère des Ressources naturelles et de la Faune, 2700, rue Einstein, Sainte-Foy, QC G1P 3W8, Canada
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