1
|
Sahoo J, Mahanty B, Mishra R, Joshi RK. Development of SNP markers linked to purple blotch resistance for marker-assisted selection in onion ( Allium cepa L.) breeding. 3 Biotech 2023; 13:137. [PMID: 37124987 PMCID: PMC10130247 DOI: 10.1007/s13205-023-03562-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 04/15/2023] [Indexed: 05/02/2023] Open
Abstract
Purple blotch (PB), caused by Alternaria porri (Ellis) Cifferi, is one of the most destructive diseases of onion worldwide. Rapid development and deployment of resistant onion varieties is the most effective approach to control this disease. A single dominant gene, ApR1 was previously linked to PB resistance in onion cultivar 'Arka Kalyan'. In this study, an advanced RIL population derived from a cross between the resistant (Arka Kalyan) and susceptible (Agrifound Rose) cultivar of onion was used to fine map the resistant locus with SNP markers. Twenty plants from the RIL population, ten each with disease resistance and susceptibility trait, were subjected to restriction site-associated DNA sequencing (RAD-Seq) and generated 7388 single nucleotide polymorphisms (SNPs). Correlation analysis between marker genotypes and PB disease phenotype on the 20 plants identified 27 SNPs as candidate markers linked to ApR1 gene for PB resistance. Six candidate SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers designated as ApRsnip5, ApRsnip8, ApRsnip14, ApRsnip21, ApRsnip23 and ApRsnip25. Marker-trait association based on disease phenotyping and KASP genotyping data on 153 RILs confirmed that all six KASP markers were tightly associated with ApR1 gene within the genetic distance of 1.3 CentiMorgan (cM). ApRsnip14 co-segregated with the ApR1 locus. Further, the six KASP markers were tested on 27 onion lines with different genetic backgrounds. ApRsnip14, ApRsnip21, ApRsnip5 and ApRsnip23 not only showed the correct resistance allele in 3 resistance genotypes, but also clustered together in the remaining 24 susceptible lines. Alternatively, ApRsnip8 and ApRsnip25 exhibited false positives in two onion lines which do not have the R-gene. Overall, our results suggest that ApRsnip14 and ApRsnip23 with their close linkage to ApR1 locus and greater applicability on breeding germplasm are recommended in marker-assisted selection for PB resistance in onion breeding program. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03562-7.
Collapse
Affiliation(s)
- Jayashree Sahoo
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
| | - Bijayalaxmi Mahanty
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
| | - Rukmini Mishra
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha India
| | - Raj Kumar Joshi
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
| |
Collapse
|
2
|
Chen Y, Li R, Sun J, Li C, Xiao H, Chen S. Genome-Wide Population Structure and Selection Signatures of Yunling Goat Based on RAD-seq. Animals (Basel) 2022; 12:ani12182401. [PMID: 36139261 PMCID: PMC9495202 DOI: 10.3390/ani12182401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/07/2022] [Accepted: 09/10/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary Goats are important domestic animals that provide meat, milk, fur, and other products for humans. The demand for these products has increased in recent years. Disease resistance among goat breeds is different, but the genetic basis of the differences in resistance to diseases is still unclear and needs to be further studied. In this study, many genes and pathways related to immunity and diseases were identified to be under positive selection between Yunling and Nubian goats using RAD-seq technology. This study on the selection signatures of Yunling goats provides the scientific basis and technical support for the breeding of domestic goats for disease resistance, which has important social and economic significance. Abstract Animal diseases impose a huge burden on the countries where diseases are endemic. Conventional control strategies of vaccines and veterinary drugs are to control diseases from a pharmaceutical perspective. Another alternative approach is using pre-existing genetic disease resistance or tolerance. We know that the Yunling goat is an excellent local breed from Yunnan, southwestern China, which has characteristics of strong disease resistance and remarkable adaptability. However, genetic information about the selection signatures of Yunling goats is limited. We reasoned that the genes underlying the observed difference in disease resistance might be identified by investigating selection signatures between two different goat breeds. Herein, we selected the Nubian goat as the reference group to perform the population structure and selection signature analysis by using RAD-seq technology. The results showed that two goat breeds were divided into two clusters, but there also existed gene flow. We used Fst (F-statistics) and π (pi/θπ) methods to carry out selection signature analysis. Eight selected regions and 91 candidate genes were identified, in which some genes such as DOK2, TIMM17A, MAVS, and DOCK8 related to disease and immunity and some genes such as SPEFI, CDC25B, and MIR103 were associated with reproduction. Four GO (Gene Ontology) terms (GO:0010591, GO:001601, GO:0038023, and GO:0017166) were associated with cell migration, signal transduction, and immune responses. The KEGG (Kyoto Encyclopedia of Genes and Genomes) signaling pathways were mainly associated with immune responses, inflammatory responses, and stress reactions. This study preliminarily revealed the genetic basis of strong disease resistance and adaptability of Yunling goats. It provides a theoretical basis for the subsequent genetic breeding of disease resistance of goats.
Collapse
Affiliation(s)
- Yuming Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China; (Y.C.); (R.L.); (C.L.); (H.X.)
- School of Life Sciences, Yunnan University, Kunming 650500, China;
| | - Rong Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China; (Y.C.); (R.L.); (C.L.); (H.X.)
- College of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Jianshu Sun
- School of Life Sciences, Yunnan University, Kunming 650500, China;
| | - Chunqing Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China; (Y.C.); (R.L.); (C.L.); (H.X.)
| | - Heng Xiao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China; (Y.C.); (R.L.); (C.L.); (H.X.)
| | - Shanyuan Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China; (Y.C.); (R.L.); (C.L.); (H.X.)
- Correspondence: ; Tel.: +86-18687122260
| |
Collapse
|
3
|
Shakouka MA, Gurjar MS, Aggarwal R, Saharan MS, Gogoi R, Bainsla Kumar N, Agarwal S, Kumar TPJ, Bayaa B, Khatib F. Genome-Wide Association Mapping of Virulence Genes in Wheat Karnal Bunt Fungus Tilletia indica Using Double Digest Restriction-Site Associated DNA-Genotyping by Sequencing Approach. Front Microbiol 2022; 13:852727. [PMID: 35633675 PMCID: PMC9139842 DOI: 10.3389/fmicb.2022.852727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Tilletia indica is a quarantine fungal pathogen that poses a serious biosecurity threat to wheat-exporting countries. Acquiring genetic data for the pathogenicity characters of T. indica is still a challenge for wheat breeders and geneticists. In the current study, double digest restriction-site associated-DNA genotyping by sequencing was carried out for 39 T. indica isolates collected from different locations in India. The generated libraries upon sequencing were with 3,346,759 raw reads on average, and 151 x 2 nucleotides read length. The obtained bases per read ranged from 87 Mb in Ti 25 to 1,708 Mb in Ti 39, with 505 Mb on average per read. Trait association mapping was performed using 41,473 SNPs, infection phenotyping data, population structure, and Kinship matrix, to find single nucleotide polymorphisms (SNPs) linked to virulence genes. Population structure analysis divided the T. indica population in India into three subpopulations with genetic mixing in each subpopulation. However, the division was not in accordance with the degree of virulence. Trait association mapping revealed the presence of 13 SNPs associated with virulence. Using sequences analysis tools, one gene (g4132) near a significant SNP was predicted to be an effector, and its relative expression was assessed and found upregulated upon infection.
Collapse
|
4
|
Che Y, He Y, Song N, Yang Y, Wei L, Yang X, Zhang Y, Zhang J, Han H, Li X, Zhou S, Liu W, Li L. Four-Year and Five-Developing-Stage Dynamic QTL Mapping for Tiller Number in the Hybrid Population of Agropyron Gaertn. FRONTIERS IN PLANT SCIENCE 2022; 13:835437. [PMID: 35283893 PMCID: PMC8907830 DOI: 10.3389/fpls.2022.835437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Tiller number (TN) is an important agronomic trait affecting gramineous crop yield. To understand the static and dynamic information of quantitative trait locus (QTLs) controlling TN of Agropyron Gaertn., both the unconditional and conditional quantitative trait loci (QTL) mapping of TN were conducted using a cross-pollinated (CP) hybrid population with a total of 113 plant lines from the cross between Agropyron cristatum (L.) Gaertn. Z1842 and Allium mongolicum Keng Z2098, based on the phenotypic data of TN at five developmental stages [i.e., recovering stage (RS), jointing stage (JS), heading stage (HS), flowering stage (FS), and maturity stage (MS)] in 4 years (i.e., 2017, 2018, 2020, and 2021) and the genetic map constructed of 1,023 single-nucleotide polymorphism (SNP) markers. Thirty-seven QTLs controlling TN were detected using two analysis methods in 4 years, which were distributed in six linkage groups. Each QTL explained 2.96-31.11% of the phenotypic variation, with a logarithum of odds (LOD) value of 2.51-13.95. Nine of these loci detected both unconditional and conditional QTLs. Twelve unconditional major QTLs and sixteen conditional major QTLs were detected. Three relatively major stable conditional QTLs, namely, cQTN1-3, cQTN1-5, and cQTN4-1, were expressed in 2020 and 2021. Meantime, two pairs of major QTLs cQTN1-5 and qTN1-4 and also cQTN2-4 and qTN2-3 were located at the same interval but in different years. Except for qTN2-2 and qTN3-5/cQTN3-5, other thirty-four QTLs were first detected in this study. This study provides a better interpretation of genetic factors that selectively control tiller at different developmental stages and a reference for molecular marker-assisted selection in the related plant improvement.
Collapse
Affiliation(s)
- Yonghe Che
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yutong He
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Nan Song
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yanping Yang
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Lai Wei
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Xinming Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinpeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haiming Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuquan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shenghui Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
5
|
Zang Y, Hu Y, Dai F, Zhang T. Comparative transcriptome analysis reveals the regulation network for fiber strength in cotton. Biotechnol Lett 2022; 44:547-560. [PMID: 35194701 DOI: 10.1007/s10529-022-03236-z] [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: 06/28/2021] [Accepted: 02/11/2022] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Determine the effect of secondary cell wall (SCW) thickness and microcrystalline cellulose content (MCC) on mature fiber strength (FS) and reveal through comparative transcriptome analysis the molecular regulation network governing FS in cotton. RESULTS Transmission electron microscope (TEM) analysis of two parent varieties, Prema with elite FS and 86-1 with weak fiber, revealed significant difference in the SCW but not in MCC. Transcriptome analysis revealed that genes differentially expressed during SCW thickening (20 DPA) are highly related to FS; in particular, up-regulated genes such as UDPG, CESA2, and NAC83 were important in SCW thickening, likely contributing to higher FS. GO and KEGG enrichment analysis revealed the common up-regulated genes to be enriched in carbon metabolism and terms relating to the cell wall. CONCLUSIONS We developed two recombinant inbred lines with elite FS, selected from the filial generation of Prema and 86-1. By comparing transcriptomic data, we revealed the gene expression network governing SCW thickness in mature fiber. Our results provide solid insights into the relationship of the SCW and FS.
Collapse
Affiliation(s)
- Yihao Zang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Plant Precision Breeding Academy, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Plant Precision Breeding Academy, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Fan Dai
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Plant Precision Breeding Academy, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Plant Precision Breeding Academy, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China. .,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
| |
Collapse
|
6
|
He JC, Li SY, He WZ, Xian JJ, Ma XY, Wang YC, Zhang MC, Ye GX, Liang B, Xia Q, Li Q. Application of Restriction Site-Associated DNA Sequencing (RAD-Seq) for Copy Number Variation and Triploidy Detection in Human. Cytogenet Genome Res 2021; 161:406-413. [PMID: 34657031 DOI: 10.1159/000518930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 08/06/2021] [Indexed: 11/19/2022] Open
Abstract
At present, low-pass whole-genome sequencing (WGS) is frequently used in clinical research and in the screening of copy number variations (CNVs). However, there are still some challenges in the detection of triploids. Restriction site-associated DNA sequencing (RAD-Seq) technology is a reduced-representation genome sequencing technology developed based on next-generation sequencing. Here, we verified whether RAD-Seq could be employed to detect CNVs and triploids. In this study, genomic DNA of 11 samples was extracted employing a routine method and used to build libraries. Five cell lines of known karyotypes and 6 triploid abortion tissue samples were included for RAD-Seq testing. The triploid samples were confirmed by STR analysis and also tested by low-pass WGS. The accuracy and efficiency of detecting CNVs and triploids by RAD-Seq were then assessed, compared with low-pass WGS. In our results, RAD-Seq detected 11 out of 11 (100%) chromosomal abnormalities, including 4 deletions and 1 aneuploidy in the purchased cell lines and all triploid samples. By contrast, these triploids were missed by low-pass WGS. Furthermore, RAD-Seq showed a higher resolution and more accurate allele frequency in the detection of triploids than low-pass WGS. Our study shows that, compared with low-pass WGS, RAD-Seq has relatively higher accuracy in CNV detection at a similar cost and is capable of identifying triploids. Therefore, the application of this technique in medical genetics has a significant potential value.
Collapse
Affiliation(s)
- Jian-Chun He
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shao-Ying Li
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wen-Zhi He
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jia-Jia Xian
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiao-Yan Ma
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yan-Chao Wang
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Min-Cong Zhang
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Guo-Xin Ye
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bo Liang
- Basecare Medical Device Co., Ltd, Suzhou, China
| | - Qin Xia
- Basecare Medical Device Co., Ltd, Suzhou, China,
| | - Qing Li
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
7
|
Zhao Y, Zhao Y, Guo Y, Su K, Shi X, Liu D, Zhang J. High-density genetic linkage-map construction of hawthorn and QTL mapping for important fruit traits. PLoS One 2020; 15:e0229020. [PMID: 32045463 PMCID: PMC7012432 DOI: 10.1371/journal.pone.0229020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/28/2020] [Indexed: 11/30/2022] Open
Abstract
Few reports exist on QTL mapping of the important economic traits of hawthorn. We hybridized the cultivars ‘Shandongdamianqiu’ (female parent) and ‘Xinbinruanzi’ (male parent), and 130 F1 individuals and the two parents were used for RAD-seq, SNP development, and high-density linkage map construction. Three genetic maps were obtained, one for each of the parents and an integrated one. In these three maps, 17 linkage groups were constructed. The female and male parent maps contained 2657 and 4088 SNP markers, respectively, and had genetic distances of 2689.65 and 2558.41 cM, respectively, whereas the integrated map was 2470.02 cM, and contained 6,384 SNP markers. QTL mapping based on six agronomic traits, namely fruit transverse diameter, vertical diameter, single fruit weight, pericarp brittleness, pericarp puncture hardness, and average sarcocarp firmness were conducted, and 25 QTLs were detected in seven linkage groups. Explained phenotypic variation rate ranged from 17.7% to 35%. This genetic map contains the largest number of molecular markers ever obtained from hawthorn and will provide an important future reference for fine QTL mapping of economic traits and molecular assisted selection of hawthorn.
Collapse
Affiliation(s)
- Yuhui Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R.C
| | - Yidi Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R.C
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R.C
- National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Shenyang, P.R.C
- * E-mail: (YG); (JZ)
| | - Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R.C
| | - Xiaochang Shi
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R.C
| | - Di Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R.C
| | - Jijun Zhang
- College of Horticulture Science and Technology, Hebei Normal University of Science and technology, Qinhuangdao, P.R.C
- * E-mail: (YG); (JZ)
| |
Collapse
|
8
|
Liu N, Guo J, Zhou X, Wu B, Huang L, Luo H, Chen Y, Chen W, Lei Y, Huang Y, Liao B, Jiang H. High-resolution mapping of a major and consensus quantitative trait locus for oil content to a ~ 0.8-Mb region on chromosome A08 in peanut (Arachis hypogaea L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:37-49. [PMID: 31559527 PMCID: PMC6952344 DOI: 10.1007/s00122-019-03438-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 09/17/2019] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE: ddRAD-seq-based high-density genetic map comprising 2595 loci identified a major and consensus QTL with a linked marker in a 0.8-Mb physical interval for oil content in peanut. Enhancing oil content is an important breeding objective in peanut. High-resolution mapping of quantitative trait loci (QTLs) with linked markers could facilitate marker-assisted selection in breeding for target traits. In the present study, a recombined inbred line population (Xuhua 13 × Zhonghua 6) was used to construct a genetic map based on double-digest restriction-site-associated DNA sequencing (ddRAD-seq). The resulting high-density genetic map contained 2595 loci, and spanned a length of 2465.62 cM, with an average distance of 0.95 cM/locus. Seven QTLs for oil content were identified on five linkage groups, including the major and stable QTL qOCA08.1 on chromosome A08 with 10.14-27.19% phenotypic variation explained. The physical interval of qOCA08.1 was further delimited to a ~ 0.8-Mb genomic region where two genes affecting oil synthesis had been annotated. The marker SNPOCA08 was developed targeting the SNP loci associated with oil content and validated in peanut cultivars with diverse oil contents. The major and stable QTL identified in the present study could be further dissected for gene discovery. Furthermore, the tightly linked marker for oil content would be useful in marker-assisted breeding in peanut.
Collapse
Affiliation(s)
- Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Bei Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China.
| |
Collapse
|
9
|
Yu K, Liu D, Chen Y, Wang D, Yang W, Yang W, Yin L, Zhang C, Zhao S, Sun J, Liu C, Zhang A. Unraveling the genetic architecture of grain size in einkorn wheat through linkage and homology mapping and transcriptomic profiling. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4671-4688. [PMID: 31226200 PMCID: PMC6760303 DOI: 10.1093/jxb/erz247] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 05/15/2019] [Indexed: 05/12/2023]
Abstract
Understanding the genetic architecture of grain size is a prerequisite to manipulating grain development and improving the potential crop yield. In this study, we conducted a whole genome-wide quantitative trait locus (QTL) mapping of grain-size-related traits by constructing a high-density genetic map using 109 recombinant inbred lines of einkorn wheat. We explored the candidate genes underlying QTLs through homologous analysis and RNA sequencing. The high-density genetic map spanned 1873 cM and contained 9937 single nucleotide polymorphism markers assigned to 1551 bins on seven chromosomes. Strong collinearity and high genome coverage of this map were revealed by comparison with physical maps of wheat and barley. Six grain size-related traits were surveyed in five environments. In total, 42 QTLs were identified; these were assigned to 17 genomic regions on six chromosomes and accounted for 52.3-66.7% of the phenotypic variation. Thirty homologous genes involved in grain development were located in 12 regions. RNA sequencing identified 4959 genes differentially expressed between the two parental lines. Twenty differentially expressed genes involved in grain size development and starch biosynthesis were mapped to nine regions that contained 26 QTLs, indicating that the starch biosynthesis pathway plays a vital role in grain development in einkorn wheat. This study provides new insights into the genetic architecture of grain size in einkorn wheat; identification of the underlying genes enables understanding of grain development and wheat genetic improvement. Furthermore, the map facilitates quantitative trait mapping, map-based cloning, genome assembly, and comparative genomics in wheat taxa.
Collapse
Affiliation(s)
- Kang Yu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yong Chen
- Science and Technology Department, State Tobacco Monopoly Administration, Beijing, China
| | - Dongzhi Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Wei Yang
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - Lixin Yin
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - Chi Zhang
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shancen Zhao
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Chunming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Correspondence: and
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- Correspondence: and
| |
Collapse
|
10
|
Yu K, Liu D, Chen Y, Wang D, Yang W, Yang W, Yin L, Zhang C, Zhao S, Sun J, Liu C, Zhang A. Unraveling the genetic architecture of grain size in einkorn wheat through linkage and homology mapping and transcriptomic profiling. JOURNAL OF EXPERIMENTAL BOTANY 2019. [PMID: 31226200 DOI: 10.1101/377820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Understanding the genetic architecture of grain size is a prerequisite to manipulating grain development and improving the potential crop yield. In this study, we conducted a whole genome-wide quantitative trait locus (QTL) mapping of grain-size-related traits by constructing a high-density genetic map using 109 recombinant inbred lines of einkorn wheat. We explored the candidate genes underlying QTLs through homologous analysis and RNA sequencing. The high-density genetic map spanned 1873 cM and contained 9937 single nucleotide polymorphism markers assigned to 1551 bins on seven chromosomes. Strong collinearity and high genome coverage of this map were revealed by comparison with physical maps of wheat and barley. Six grain size-related traits were surveyed in five environments. In total, 42 QTLs were identified; these were assigned to 17 genomic regions on six chromosomes and accounted for 52.3-66.7% of the phenotypic variation. Thirty homologous genes involved in grain development were located in 12 regions. RNA sequencing identified 4959 genes differentially expressed between the two parental lines. Twenty differentially expressed genes involved in grain size development and starch biosynthesis were mapped to nine regions that contained 26 QTLs, indicating that the starch biosynthesis pathway plays a vital role in grain development in einkorn wheat. This study provides new insights into the genetic architecture of grain size in einkorn wheat; identification of the underlying genes enables understanding of grain development and wheat genetic improvement. Furthermore, the map facilitates quantitative trait mapping, map-based cloning, genome assembly, and comparative genomics in wheat taxa.
Collapse
Affiliation(s)
- Kang Yu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yong Chen
- Science and Technology Department, State Tobacco Monopoly Administration, Beijing, China
| | - Dongzhi Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Wei Yang
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - Lixin Yin
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - Chi Zhang
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shancen Zhao
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Chunming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
11
|
Li GH, Chen HC, Liu JL, Luo WL, Xie DS, Luo SB, Wu TQ, Akram W, Zhong YJ. A high-density genetic map developed by specific-locus amplified fragment (SLAF) sequencing and identification of a locus controlling anthocyanin pigmentation in stalk of Zicaitai (Brassica rapa L. ssp. chinensis var. purpurea). BMC Genomics 2019; 20:343. [PMID: 31064320 PMCID: PMC6503552 DOI: 10.1186/s12864-019-5693-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/15/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Caixin and Zicaitai (Brassica rapa) belong to Southern and Central China respectively. Zicaitai contains high amount of anthocyanin in leaf and stalk resulting to the purple color. Stalk is the major edible part and stalk color is an economically important trait for the two vegetables. The aim of this study is to construct a high density genetic map using the specific length amplified fragment sequencing (SLAF-seq) technique to explore genetic basis for anthocyanin pigmentation traits via quantitative trait loci (QTL) mapping. RESULTS We constructed a high generation linkage map with a mapping panel of F2 populations derived from 150 individuals of parental lines "Xianghongtai 01" and "Yinong 50D" with purple and green stalk respectively. The map was constructed containing 4253 loci, representing 10,940 single nucleotide polymorphism (SNP) markers spanning 1030.04 centiMorgans (cM) over 10 linkage groups (LGs), with an average distance between markers of 0.27 cM. Quantitative trait loci (QTL) analysis revealed that a major locus on chromosome 7 and 4 minor QTLs explaining 2.69-61.21% of phenotypic variation (PVE) were strongly responsible for variation in stalk color trait. Bioinformatics analysis of the major locus identified 62 protein-coding genes. Among the major locus, there were no biosynthetic genes related to anthocyanin. However, there were several transcription factors like helix-loop-helix (bHLH) bHLH, MYB in the locus. Seven predicted candidate genes were selected for the transcription level analysis. Only bHLH49 transcription factor, was significantly higher expressed in both stalks and young leaves of Xianghongtai01 than Yinong50D. An insertion and deletion (InDel) marker developed from deletion/insertion in the promoter region of bHLH49 showed significant correlation with the stalk color trait in the F2 population. CONCLUSION Using the constructed high-qualified linkage map, this study successfully identified QTLs for stalk color trait. The identified valuable markers and candidate genes for anthocyanin accumulation in stalk will provide useful information for molecular regulation of anthocyanin biosynthesis. Overall our findings will lay a foundation for functional gene cloning, marker-assisted selection (MAS) and molecular breeding of important economic traits in B. rapa.
Collapse
Affiliation(s)
- Gui-Hua Li
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Han-Cai Chen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China
| | - Jia-Li Liu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Wen-Long Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Da-Sen Xie
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Shao-Bo Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Ting-Quan Wu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Waheed Akram
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Yu-Juan Zhong
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China. .,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China.
| |
Collapse
|
12
|
Zheng X, Tang Y, Ye J, Pan Z, Tan M, Xie Z, Chai L, Xu Q, Fraser PD, Deng X. SLAF-Based Construction of a High-Density Genetic Map and Its Application in QTL Mapping of Carotenoids Content in Citrus Fruit. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:994-1002. [PMID: 30589260 DOI: 10.1021/acs.jafc.8b05176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Carotenoids are important antioxidant components in the human diet. To develop carotenoid-rich agricultural products by genetic intervention, understanding the genetic basis of carotenoids variation is essential. In this study, we constructed a high-density integrated genetic map with 3817 molecular markers using specific locus amplified fragment (SLAF) sequencing from a C. reticulata × P. trifoliata F1 pseudotestcross population. A total of 17 significant quantitative trait loci (QTLs) distributed on Chromosomes (Chr) 2, 3, 5, 6, and 9 were detected to determine the carotenoid variation in the population. In particular, three QTL colocalizations for multiple carotenoid constituents were observed on Chr 2, 3, and 9, one of which was located on Chr2:34,654,608-35430715 accounted for 20.1-25.4% of the variation of luteoxanthin, auroxanthin, lutein, violaxanthin, and total carotenoid content. Overall, this study provides a genetic foundation for marker-assisted selection (MAS) breeding of nutritionally enhanced citrus fruit.
Collapse
Affiliation(s)
- Xiongjie Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Yuqing Tang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Junli Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Zhiyong Pan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Meilian Tan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Zongzhou Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Lijun Chai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway , University of London , Egham, Surrey TW20 0EX , United Kingdom
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| |
Collapse
|
13
|
Zhu J, Guo Y, Su K, Liu Z, Ren Z, Li K, Guo X. Construction of a highly saturated Genetic Map for Vitis by Next-generation Restriction Site-associated DNA Sequencing. BMC PLANT BIOLOGY 2018; 18:347. [PMID: 30541441 PMCID: PMC6291968 DOI: 10.1186/s12870-018-1575-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/26/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND High-saturate molecular linkage maps are an important tool in studies on plant molecular biology and assisted breeding. Development of a large set of single nucleotide polymorphisms (SNPs) via next-generation sequencing (NGS)-based methods, restriction-site associated DNA sequencing (RAD-seq), and the generation of a highly saturated genetic map help improve fine mapping of quantitative trait loci (QTL). RESULTS We generated a highly saturated genetic map to identify significant traits in two elite grape cultivars and 176 F1 plants. In total, 1,426,967 high-quality restriction site-associated DNA tags were detected; 51,365, 23,683, and 70,061 markers were assessed in 19 linkage groups (LGs) for the maternal, paternal, and integrated maps, respectively. Our map was highly saturated in terms of marker density and average "Gap ≤ 5 cM" percentage. CONCLUSIONS In this study, RAD-seq of 176 F1 plants and their parents yielded 8,481,484 SNPs and 1,646,131 InDel markers, of which 65,229 and 4832, respectively, were used to construct a highly saturated genetic map for grapevine. This map is expected to facilitate genetic studies on grapevine, including an evaluation of grapevine and deciphering the genetic basis of economically and agronomically important traits. Our findings provide basic essential genetic data the grapevine genetic research community, which will lead to improvements in grapevine breeding.
Collapse
Affiliation(s)
- Junchi Zhu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
- Ministry of Education Key Laboratory of Protected Horticulture, Shenyang, 110866 People’s Republic of China
| | - Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| | - Zhendong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| | - Zhihua Ren
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| | - Kun Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| | - Xiuwu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| |
Collapse
|
14
|
A Multi-Level Strategy Based on Metabolic and Molecular Genetic Approaches for the Characterization of Different Coptis Medicines Using HPLC-UV and RAD-seq Techniques. Molecules 2018; 23:molecules23123090. [PMID: 30486378 PMCID: PMC6321400 DOI: 10.3390/molecules23123090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/23/2018] [Accepted: 11/24/2018] [Indexed: 12/19/2022] Open
Abstract
Coptis plants (Ranunculaceae) to have played an important role in the prevention and treatment human diseases in Chinese history. In this study, a multi-level strategy based on metabolic and molecular genetic methods was performed for the characterization of four Coptis herbs (C. chinensis, C. deltoidea, C. omeiensis and C. teeta) using high performance liquid chromatography-ultraviolet (HPLC-UV) and restriction site-associated DNA sequencing (RAD-seq) techniques. Protoberberine alkaloids including berberine, palmatine, coptisine, epiberberine, columbamine, jatrorrhizine, magnoflorine and groenlandicine in rhizomes were identified and determined based on the HPLC-UV method. Among them, berberine was demonstrated as the most abundant compound in these plants. RAD-seq was applied to discover single nucleotide polymorphisms (SNPs) data. A total of 44,747,016 reads were generated and 2,443,407 SNPs were identified in regarding to four plants. Additionally, with respect to complicated metabolic and SNP data, multivariable statistical methods of principal component analysis (PCA) and hierarchical cluster analysis (HCA) were successively applied to interpret the structure characteristics. The metabolic variation and genetic relationship among different Coptis plants were successfully illustrated based on data visualization. Summarily, this comprehensive strategy has been proven as a reliable and effective approach to characterize Coptis plants, which can provide additional information for their quality assessment.
Collapse
|
15
|
Yao D, Wu H, Chen Y, Yang W, Gao H, Tong C. gmRAD: an integrated SNP calling pipeline for genetic mapping with RADseq across a hybrid population. Brief Bioinform 2018; 21:329-337. [PMID: 30445432 DOI: 10.1093/bib/bby114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/21/2018] [Accepted: 10/23/2018] [Indexed: 11/14/2022] Open
Abstract
Restriction site-associated DNA sequencing (RADseq) is a powerful technology that has been extensively applied in population genetics, phylogenetics and genetic mapping. Although many software packages are available for ecological and evolutionary studies, a few effective tools are available for extracting genotype data with RADseq for genetic mapping, a prerequisite for quantitative trait locus mapping, comparative genomics and genome scaffold assembly. Here, we present an integrated pipeline called gmRAD for generating single nucleotide polymorphism (SNP) genotypes from RADseq data, de novo, across a genetic mapping population derived by crossing two parents. As an analytical strategy, the software takes five steps to implement the whole algorithms, including clustering the first (forward) reads of each parent, building two parental references, generating parental SNP catalogs, calling SNP genotypes across all individuals and filtering the genotype data for genetic linkage mapping. All the steps can be completed with a simple command line, but they can be also performed optionally if prerequisite files are available. To validate its application, we also performed a real data analysis with RADseq data from an F1 hybrid population derived by crossing Populus deltoides and Populus simonii. The software gmRAD is freely available at https://github.com/tongchf/gmRAD.
Collapse
Affiliation(s)
- Dan Yao
- Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Hainan Wu
- Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yuhua Chen
- Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Wenguo Yang
- Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Hua Gao
- Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Chunfa Tong
- Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
16
|
Che Y, Song N, Yang Y, Yang X, Duan Q, Zhang Y, Lu Y, Li X, Zhang J, Li X, Zhou S, Li L, Liu W. QTL Mapping of Six Spike and Stem Traits in Hybrid Population of Agropyron Gaertn. in Multiple Environments. FRONTIERS IN PLANT SCIENCE 2018; 9:1422. [PMID: 30425721 PMCID: PMC6218563 DOI: 10.3389/fpls.2018.01422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 09/06/2018] [Indexed: 05/31/2023]
Abstract
Most Agropyron Gaertn. species are excellent sources of forage. The derivative lines of wheat-Agropyron cristatum show elite agronomic traits, and some are valuable for wheat breeding. The species of Agropyron Gaertn. was mainly recognized by the spike morphology in traditional taxon. Six traits, including spike length (SL), ear stem length (ESL), the second internodes length (SIL), spikelet number per spike (SNS), floret number per spikelet (FNS), and grain number per spikelet (GNS), are vital to morphology studies and also influences the forage crop yield. To elucidate the genetic basis of spike and stem traits, a quantitative trait locus (QTL) analysis was conducted in a cross-pollinated (CP) hybrid population derived from a cross between two diverse parents, Agropyron mongolicum Keng Z2098 and A. cristatum (L.) Gaertn. Z1842, evaluated across three ecotopes (Langfang, Changli, and Guyuan of Hebei, China) over 3 years (from 2014 to 2016). Construction of a high-density linkage map was based on 1,023 single-nucleotide polymorphism (SNP) markers, covering 907.8 cM of the whole Agropyron genome. A total of 306 QTLs with single QTL in different environments explaining 0.07-33.21% of the phenotypic variation were detected for study traits. Seven major-effect QTLs were identified, including one for ESL on chromosome 3, one for SIL on chromosome 5, three for SL (two on chromosome 2 and one on chromosome 4), and two for SNS on chromosomes 3 and 7. Also, seven stable QTLs, including four for ESL, one for SL, one for GNS, and one for FNS, were mainly mapped on chromosomes 2, 3, 4, 5, and 7, respectively, elucidating 0.25-14.98% of the phenotypic variations. On the use of Agropyron CP hybrid population to identify QTL determining spike and stem traits for the first time, these QTLs for six traits would provide a theoretical reference for the molecular marker-assisted selection in the improvement of forage and cereal crop species.
Collapse
Affiliation(s)
- Yonghe Che
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Nan Song
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yanping Yang
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Xinming Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingqing Duan
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuqing Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuqing Li
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jinpeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuquan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shenghui Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
17
|
Feng JY, Li M, Zhao S, Zhang C, Yang ST, Qiao S, Tan WF, Qu HJ, Wang DY, Pu ZG. Analysis of evolution and genetic diversity of sweetpotato and its related different polyploidy wild species I. trifida using RAD-seq. BMC PLANT BIOLOGY 2018; 18:181. [PMID: 30185158 PMCID: PMC6126004 DOI: 10.1186/s12870-018-1399-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 08/28/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Sweetpotato (Ipomoea batatas (L.) Lam.) is one of the most important crops from the family of Convolvulaceae. It is widely reported that cultivated sweetpotato was originated from Ipomoea trifida. However, diploid, tetraploid and hexaploid I. trifida were found in nature. The relationship, between them, and among them and sweetpotato, is remaining unclear. RESULTS In the present study, we detected the genome diversity and relationship of sweetpotato and different polyploidy types I. trifida using Restriction-site Associated DNA Sequencing (RAD-seq). A total of 38,605 RAD-tags containing 832,204 SNPs had been identified. These tags were annotated using five public databases, about 11,519 tags were aligned to functional genes in various pathways. Based on SNP genotype, phylogenetic relation analysis results confirmed that cultivated sweetpotato has a closer relationship with I. trifida 6× than with I. trifida 4X and I. trifida 2×. Besides, 5042 SSRs were detected in I. trifida 6×, and 3202 pairs of high-quality SSR primers were developed. A total of 68 primers were randomly selected and synthesized, of which 61 were successfully amplified. CONCLUSION These results provided new evidence that cultivated sweetpotato originated from I. trifida 6×, and that I. trifida 6× evolved from I. trifida 4X and I. trifida 2×. Therefore, using I. trifida 6× as the model plant of sweetpotato research should be more practical than using I. trifida 2× in the future. Meanwhile, sequence information and markers from the present study will be helpful for sweetpotato and I. trifida studies in the future.
Collapse
Affiliation(s)
- J Y Feng
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, China.
| | - M Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, China
| | - S Zhao
- Center of Analysis and Testing, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, China
| | - C Zhang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, China
| | - S T Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - S Qiao
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - W F Tan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - H J Qu
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, China
| | - D Y Wang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Z G Pu
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, China.
| |
Collapse
|
18
|
Guo S, Iqbal S, Ma R, Song J, Yu M, Gao Z. High-density genetic map construction and quantitative trait loci analysis of the stony hard phenotype in peach based on restriction-site associated DNA sequencing. BMC Genomics 2018; 19:612. [PMID: 30107781 PMCID: PMC6092793 DOI: 10.1186/s12864-018-4952-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 07/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Peach (Prunus persica) is an important fruit crop that generally softens rapidly after harvest resulting in a short shelf-life. By contrast, stony hard (SH) peach fruit does not soften and hardly produces ethylene. To explore the candidate genes responsible for the SH phenotype, a high-density genetic map was constructed by restriction-site associated DNA sequencing technology. RESULTS In the present study, the linkage map consisted of 1310 single nucleotide polymorphism markers, spanning 454.2 cM, with an average marker distance of 0.347 cM. The single nucleotide polymorphisms were able to anchor eight linkage groups to their corresponding chromosomes. Based on this high-density integrated peach linkage map and two years of fruit phenotyping, two potential quantitative trait loci for the SH trait were identified and positioned on the genetic map. Additionally, Prupe.6G150900.1, a key gene in abscisic acid (ABA) biosynthesis, displayed a differential expression profile identical to the ABA accumulation pattern: mRNA transcripts were maintained at a high level during storage of SH peaches but occurred at low levels in melting fruit. CONCLUSION Thus Prupe.6G150900.1 might play a crucial role in the SH phenotype of peach in which ABA negatively regulates ethylene production. Also, this high-density linkage map of peach will contribute to the mapping of important fruit traits and quantitative trait loci identification.
Collapse
Affiliation(s)
- Shaolei Guo
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- Jiangsu Key Laboratory of Horticultural Crop Genetic Improvement, Nanjing, 210014, China
| | - Shahid Iqbal
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruijuan Ma
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- Jiangsu Key Laboratory of Horticultural Crop Genetic Improvement, Nanjing, 210014, China
| | - Juan Song
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- Jiangsu Key Laboratory of Horticultural Crop Genetic Improvement, Nanjing, 210014, China
| | - Mingliang Yu
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
- Jiangsu Key Laboratory of Horticultural Crop Genetic Improvement, Nanjing, 210014, China.
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
19
|
Yu X, Yang D, Guo C, Gao L. Plant phylogenomics based on genome-partitioning strategies: Progress and prospects. PLANT DIVERSITY 2018; 40:158-164. [PMID: 30740560 PMCID: PMC6137260 DOI: 10.1016/j.pld.2018.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 05/26/2023]
Abstract
The rapid expansion of next-generation sequencing (NGS) has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genome-partitioning approaches in plant phylogenomics: genome skimming, transcriptome sequencing (RNA-seq), restriction site associated DNA sequencing (RAD-Seq), and targeted capture (Hyb-seq). Of these four genome-partitioning approaches, targeted capture (especially Hyb-seq) shows the greatest promise for plant phylogenetics over the next few years. This review will aid researchers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion of whole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research.
Collapse
Affiliation(s)
- Xiangqin Yu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Dan Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Lianming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| |
Collapse
|
20
|
Xie M, Ming Y, Shao F, Jian J, Zhang Y, Peng Z. Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish ( Silurus meridionalis). ROYAL SOCIETY OPEN SCIENCE 2018; 5:172054. [PMID: 29892392 PMCID: PMC5990832 DOI: 10.1098/rsos.172054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
Single-nucleotide polymorphism (SNP) markers and high-density genetic maps are important resources for marker-assisted selection, mapping of quantitative trait loci (QTLs) and genome structure analysis. Although linkage maps in certain catfish species have been obtained, high-density maps remain unavailable in the economically important southern catfish (Silurus meridionalis). Recently developed restriction site-associated DNA (RAD) markers have proved to be a promising tool for SNP detection and genetic map construction. The objective of the present study was to construct a high-density linkage map using SNPs generated by next-generation RAD sequencing in S. meridionalis for future genetic and genomic studies. An F1 population of 100 individuals was obtained by intraspecific crossing of two wild heterozygous individuals. In total, 77 634 putative high-quality bi-allelic SNPs between the parents were discovered by mapping the parents' paired-end RAD reads onto the reference contigs from both parents, of which 54.7% were transitions and 45.3% were transversions (transition/transversion ratio of 1.2). Finally, 26 714 high-quality RAD markers were grouped into 29 linkage groups by using de novo clustering methods (Stacks). Among these markers, 4514 were linked to the female genetic map, 23 718 to the male map and 6715 effective loci were linked to the integrated map spanning 5918.31 centimorgans (cM), with an average marker interval of 0.89 cM. High-resolution genetic maps are a useful tool for both marker-assisted breeding and various genome investigations in catfish, such as sequence assembly, gene localization, QTL detection and genome structure comparison. Hence, such a high-density linkage map will serve as a valuable resource for comparative genomics and fine-scale QTL mapping in catfish species.
Collapse
Affiliation(s)
- Mimi Xie
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, People's Republic of China
| | - Yao Ming
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, People's Republic of China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, People's Republic of China
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, People's Republic of China
| | - Yaoguang Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, People's Republic of China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, People's Republic of China
| |
Collapse
|
21
|
Cui J, Luo S, Niu Y, Huang R, Wen Q, Su J, Miao N, He W, Dong Z, Cheng J, Hu K. A RAD-Based Genetic Map for Anchoring Scaffold Sequences and Identifying QTLs in Bitter Gourd ( Momordica charantia). FRONTIERS IN PLANT SCIENCE 2018; 9:477. [PMID: 29706980 PMCID: PMC5906717 DOI: 10.3389/fpls.2018.00477] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 03/27/2018] [Indexed: 05/22/2023]
Abstract
Genetic mapping is a basic tool necessary for anchoring assembled scaffold sequences and for identifying QTLs controlling important traits. Though bitter gourd (Momordica charantia) is both consumed and used as a medicinal, research on its genomics and genetic mapping is severely limited. Here, we report the construction of a restriction site associated DNA (RAD)-based genetic map for bitter gourd using an F2 mapping population comprising 423 individuals derived from two cultivated inbred lines, the gynoecious line 'K44' and the monoecious line 'Dali-11.' This map comprised 1,009 SNP markers and spanned a total genetic distance of 2,203.95 cM across the 11 linkage groups. It anchored a total of 113 assembled scaffolds that covered about 251.32 Mb (85.48%) of the 294.01 Mb assembled genome. In addition, three horticulturally important traits including sex expression, fruit epidermal structure, and immature fruit color were evaluated using a combination of qualitative and quantitative data. As a result, we identified three QTL/gene loci responsible for these traits in three environments. The QTL/gene gy/fffn/ffn, controlling sex expression involved in gynoecy, first female flower node, and female flower number was detected in the reported region. Particularly, two QTLs/genes, Fwa/Wr and w, were found to be responsible for fruit epidermal structure and white immature fruit color, respectively. This RAD-based genetic map promotes the assembly of the bitter gourd genome and the identified genetic loci will accelerate the cloning of relevant genes in the future.
Collapse
Affiliation(s)
- Junjie Cui
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Shaobo Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yu Niu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Rukui Huang
- Vegetable Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Qingfang Wen
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jianwen Su
- Hunan Vegetable Research Institute, Changsha, China
| | - Nansheng Miao
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Weiming He
- Beijing Genomics Institute, Shenzhen, China
| | | | - Jiaowen Cheng
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
| |
Collapse
|
22
|
Cai Z, Cheng Y, Ma Z, Liu X, Ma Q, Xia Q, Zhang G, Mu Y, Nian H. Fine-mapping of QTLs for individual and total isoflavone content in soybean (Glycine max L.) using a high-density genetic map. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:555-568. [PMID: 29159422 DOI: 10.1007/s00122-017-3018-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 11/04/2017] [Indexed: 06/07/2023]
Abstract
KEY MESSAGE Fifteen stable QTLs were identified using a high-density soybean genetic map across multiple environments. One major QTL, qIF5-1, contributing to total isoflavone content explained phenotypic variance 49.38, 43.27, 46.59, 45.15 and 52.50%, respectively. Soybeans (Glycine max L.) are a major source of dietary isoflavones. To identify novel quantitative trait loci (QTL) underlying isoflavone content, and to improve the accuracy of marker-assisted breeding in soybean, a valuable mapping population comprised of 196 F7:8-10 recombinant inbred lines (RILs, Huachun 2 × Wayao) was utilized to evaluate individual and total isoflavone content in plants grown in four different environments in Guangdong. A high-density genetic linkage map containing 3469 recombination bin markers based on 0.2 × restriction site-associated DNA tag sequencing (RAD-seq) technology was used to finely map QTLs for both individual and total isoflavone contents. Correlation analyses showed that total isoflavone content, and that of five individual isoflavone, was significantly correlated across the four environments. Based on the high-density genetic linkage map, a total of 15 stable quantitative trait loci (QTLs) associated with isoflavone content across multiple environments were mapped onto chromosomes 02, 05, 07, 09, 10, 11, 13, 16, 17, and 19. Further, one of them, qIF5-1, localized to chromosomes 05 (38,434,171-39,045,620 bp) contributed to almost all isoflavone components across all environments, and explained 6.37-59.95% of the phenotypic variance, especially explained 49.38, 43.27, 46.59, 45.15 and 52.50% for total isoflavone. The results obtained in the present study will pave the way for a better understanding of the genetics of isoflavone accumulation and reveals the scope available for improvement of isoflavone content through marker-assisted selection.
Collapse
Affiliation(s)
- Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- Shofine Seed Technology Co., Ltd., Jiaxiang, 272400, Shandong, People's Republic of China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- Shofine Seed Technology Co., Ltd., Jiaxiang, 272400, Shandong, People's Republic of China
| | - Zhuwen Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Xinguo Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- Shofine Seed Technology Co., Ltd., Jiaxiang, 272400, Shandong, People's Republic of China
| | - Qiuju Xia
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518086, People's Republic of China
| | - Gengyun Zhang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518086, People's Republic of China
| | - Yinghui Mu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
- Shofine Seed Technology Co., Ltd., Jiaxiang, 272400, Shandong, People's Republic of China.
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
- Shofine Seed Technology Co., Ltd., Jiaxiang, 272400, Shandong, People's Republic of China.
| |
Collapse
|
23
|
Xia Z, Zhang S, Wen M, Lu C, Sun Y, Zou M, Wang W. Construction of an ultrahigh-density genetic linkage map for Jatropha curcas L. and identification of QTL for fruit yield. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:3. [PMID: 29321812 PMCID: PMC5759280 DOI: 10.1186/s13068-017-1004-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 12/22/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND As an important biofuel plant, the demand for higher yield Jatropha curcas L. is rapidly increasing. However, genetic analysis of Jatropha and molecular breeding for higher yield have been hampered by the limited number of molecular markers available. RESULTS An ultrahigh-density linkage map for a Jatropha mapping population of 153 individuals was constructed and covered 1380.58 cM of the Jatropha genome, with average marker density of 0.403 cM. The genetic linkage map consisted of 3422 SNP and indel markers, which clustered into 11 linkage groups. With this map, 13 repeatable QTLs (reQTLs) for fruit yield traits were identified. Ten reQTLs, qNF-1, qNF-2a, qNF-2b, qNF-2c, qNF-3, qNF-4, qNF-6, qNF-7a, qNF-7b and qNF-8, that control the number of fruits (NF) mapped to LGs 1, 2, 3, 4, 6, 7 and 8, whereas three reQTLs, qTWF-1, qTWF-2 and qTWF-3, that control the total weight of fruits (TWF) mapped to LGs 1, 2 and 3, respectively. It is interesting that there are two candidate critical genes, which may regulate Jatropha fruit yield. We also identified three pleiotropic reQTL pairs associated with both the NF and TWF traits. CONCLUSION This study is the first to report an ultrahigh-density Jatropha genetic linkage map construction, and the markers used in this study showed great potential for QTL mapping. Thirteen fruit-yield reQTLs and two important candidate genes were identified based on this linkage map. This genetic linkage map will be a useful tool for the localization of other economically important QTLs and candidate genes for Jatropha.
Collapse
Affiliation(s)
- Zhiqiang Xia
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Huazhong Agricultural University, Wuhan, China
| | - Shengkui Zhang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Huazhong Agricultural University, Wuhan, China
| | - Mingfu Wen
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Cheng Lu
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Yufang Sun
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Meiling Zou
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Huazhong Agricultural University, Wuhan, China
| | - Wenquan Wang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| |
Collapse
|
24
|
Zaccaron M, Sharma S, Bluhm BH. MoNSTR-seq, a restriction site-associated DNA sequencing technique to characterize Agrobacterium-mediated transfer-DNA insertions in Phomopsis longicolla. Lett Appl Microbiol 2018; 66:19-24. [PMID: 29108115 DOI: 10.1111/lam.12817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 10/14/2017] [Accepted: 10/24/2017] [Indexed: 11/26/2022]
Abstract
Phomopsis longicolla (Hobbs) causes Phomopsis seed decay and stem lesions in soybean (Glycine max). In this study, a novel, high-throughput adaptation of RAD-seq termed MoNSTR-seq (Mutation analysis via Next-generation DNA Sequencing of T-DNA Regions) was developed to determine the genomic location of T-DNA insertions in P. longicolla mutants. Insertional mutants were created via Agrobacterium tumefaciens-mediated transformation, and one mutant, strain PL343, was further investigated due to impaired stem lesion formation. Mutation analysis via Next-generation DNA Sequencing of T-DNA Regions, in which DNA libraries are created with two distinct restriction enzymes and customized adapters to simultaneously enrich both T-DNA insertion borders, was developed to characterize the genomic lesion in strain PL343. MoNSTR-seq successfully identified a T-DNA insertion in the predicted promoter region of a gene encoding a cellobiose dehydrogenase (CDH1), and the position of the T-DNA insertion in strain PL343 was confirmed by Sanger sequencing. Thus, MoNSTR-seq represents an effective tool for molecular genetics in P. longicolla, and is readily adaptable for use in diverse fungal species. SIGNIFICANCE AND IMPACT OF THE STUDY This study describes MoNSTR-seq (Mutation analysis via Next-generation DNA Sequencing of T-DNA Regions), an adaptation of restriction site-associated DNA sequencing (RAD-seq) to identify the position of transfer-DNA (T-DNA) insertions in the genome of Phomopsis longicolla, an important pathogen of soybean. The technique enables high-throughput characterization of mutants generated via Agrobacterium tumefaciens-mediated transformation (ATMT), thus accelerating gene discovery via forward genetics. This technique represents a significant advancement over existing approaches to characterize T-DNA insertions in fungal genomes. With minor modifications, this technique could be easily adapted to taxonomically diverse fungal pathogens and additional mutagenesis cassettes.
Collapse
Affiliation(s)
- M Zaccaron
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, USA
| | - S Sharma
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, USA
| | - B H Bluhm
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, USA
| |
Collapse
|
25
|
Arafa RA, Rakha MT, Soliman NEK, Moussa OM, Kamel SM, Shirasawa K. Rapid identification of candidate genes for resistance to tomato late blight disease using next-generation sequencing technologies. PLoS One 2017; 12:e0189951. [PMID: 29253902 PMCID: PMC5734779 DOI: 10.1371/journal.pone.0189951] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/05/2017] [Indexed: 11/19/2022] Open
Abstract
Tomato late blight caused by Phytophthora infestans (Mont.) de Bary, also known as the Irish famine pathogen, is one of the most destructive plant diseases. Wild relatives of tomato possess useful resistance genes against this disease, and could therefore be used in breeding to improve cultivated varieties. In the genome of a wild relative of tomato, Solanum habrochaites accession LA1777, we identified a new quantitative trait locus for resistance against blight caused by an aggressive Egyptian isolate of P. infestans. Using double-digest restriction site-associated DNA sequencing (ddRAD-Seq) technology, we determined 6,514 genome-wide SNP genotypes of an F2 population derived from an interspecific cross. Subsequent association analysis of genotypes and phenotypes of the mapping population revealed that a 6.8 Mb genome region on chromosome 6 was a candidate locus for disease resistance. Whole-genome resequencing analysis revealed that 298 genes in this region potentially had functional differences between the parental lines. Among of them, two genes with missense mutations, Solyc06g071810.1 and Solyc06g083640.3, were considered to be potential candidates for disease resistance. SNP and SSR markers linking to this region can be used in marker-assisted selection in future breeding programs for late blight disease, including introgression of new genetic loci from wild species. In addition, the approach developed in this study provides a model for identification of other genes for attractive agronomical traits.
Collapse
Affiliation(s)
- Ramadan A. Arafa
- Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Mohamed T. Rakha
- Department of Horticulture, Faculty of Agriculture, University of Kafrelsheikh, Kafr El-Sheikh, Egypt
| | - Nour Elden K. Soliman
- Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Olfat M. Moussa
- Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Said M. Kamel
- Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Kenta Shirasawa
- Department of Frontier Science, Kazusa DNA Research Institute, Chiba, Japan
| |
Collapse
|
26
|
Pan L, Wang N, Wu Z, Guo R, Yu X, Zheng Y, Xia Q, Gui S, Chen C. A High Density Genetic Map Derived from RAD Sequencing and Its Application in QTL Analysis of Yield-Related Traits in Vigna unguiculata. FRONTIERS IN PLANT SCIENCE 2017; 8:1544. [PMID: 28936219 PMCID: PMC5594218 DOI: 10.3389/fpls.2017.01544] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/23/2017] [Indexed: 05/29/2023]
Abstract
Cowpea [Vigna unguiculata (L.) Walp.] is an annual legume of economic importance and widely grown in the semi-arid tropics. However, high-density genetic maps of cowpea are still lacking. Here, we identified 34,868 SNPs (single nucleotide polymorphisms) that were distributed in the cowpea genome based on the RAD sequencing (restriction-site associated DNA sequencing) technique using a population of 170 individuals (two cowpea parents and 168 F2:3 progenies). Of these, 17,996 reliable SNPs were allotted to 11 consensus linkage groups (LGs). The length of the genetic map was 1,194.25 cM in total with a mean distance of 0.066 cM/SNP marker locus. Using this map and the F2:3 population, combined with the CIM (composite interval mapping) method, eleven quantitative trait loci (QTL) of yield-related trait were detected on seven LGs (LG4, 5, 6, 7, 9, 10, and 11) in cowpea. These QTL explained 0.05-17.32% of the total phenotypic variation. Among these, four QTL were for pod length, four QTL for thousand-grain weight (TGW), two QTL for grain number per pod, and one QTL for carpopodium length. Our results will provide a foundation for understanding genes related to grain yield in the cowpea and genus Vigna.
Collapse
Affiliation(s)
- Lei Pan
- Hubei Province Engineering Research Centre of Legume Plants, College of Life Sciences, Jianghan UniversityWuhan, China
| | - Nian Wang
- Department of Forestry, College of Horticulture and Forest, Huazhong Agriculture UniversityWuhan, China
| | - Zhihua Wu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Rui Guo
- Hubei Province Engineering Research Centre of Legume Plants, College of Life Sciences, Jianghan UniversityWuhan, China
| | - Xiaolu Yu
- Hubei Province Engineering Research Centre of Legume Plants, College of Life Sciences, Jianghan UniversityWuhan, China
| | - Yu Zheng
- Institute for Interdisciplinary Research, Jianghan UniversityWuhan, China
| | | | - Songtao Gui
- Department of Genetics, State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
| | - Chanyou Chen
- Hubei Province Engineering Research Centre of Legume Plants, College of Life Sciences, Jianghan UniversityWuhan, China
| |
Collapse
|
27
|
Kumar J, Gupta DS, Gupta S, Dubey S, Gupta P, Kumar S. Quantitative trait loci from identification to exploitation for crop improvement. PLANT CELL REPORTS 2017; 36:1187-1213. [PMID: 28352970 DOI: 10.1007/s00299-017-2127-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/09/2017] [Indexed: 05/24/2023]
Abstract
Advancement in the field of genetics and genomics after the discovery of Mendel's laws of inheritance has led to map the genes controlling qualitative and quantitative traits in crop plant species. Mapping of genomic regions controlling the variation of quantitatively inherited traits has become routine after the advent of different types of molecular markers. Recently, the next generation sequencing methods have accelerated the research on QTL analysis. These efforts have led to the identification of more closely linked molecular markers with gene/QTLs and also identified markers even within gene/QTL controlling the trait of interest. Efforts have also been made towards cloning gene/QTLs or identification of potential candidate genes responsible for a trait. Further new concepts like crop QTLome and QTL prioritization have accelerated precise application of QTLs for genetic improvement of complex traits. In the past years, efforts have also been made in exploitation of a number of QTL for improving grain yield or other agronomic traits in various crops through markers assisted selection leading to cultivation of these improved varieties at farmers' field. In present article, we reviewed QTLs from their identification to exploitation in plant breeding programs and also reviewed that how improved cultivars developed through introgression of QTLs have improved the yield productivity in many crops.
Collapse
Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sunanda Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sonali Dubey
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Priyanka Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat-Institutes, B.P. 6299, Rabat, Morocco
| |
Collapse
|
28
|
Wang J, Su K, Guo Y, Xing H, Zhao Y, Liu Z, Li K, Guo X. Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing. PLoS One 2017; 12:e0181728. [PMID: 28746364 PMCID: PMC5528875 DOI: 10.1371/journal.pone.0181728] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/06/2017] [Indexed: 12/30/2022] Open
Abstract
Genetic maps are important tools in plant genomics and breeding. We report a large-scale discovery of single nucleotide polymorphisms (SNPs) using the specific length amplified fragment sequencing (SLAF-seq) technique for the construction of high-density genetic maps for two elite wine grape cultivars, ‘Chardonnay’ and ‘Beibinghong’, and their 130 F1 plants. A total of 372.53 M paired-end reads were obtained after preprocessing. The average sequencing depth was 33.81 for ‘Chardonnay’ (the female parent), 48.20 for ‘Beibinghong’ (the male parent), and 12.66 for the F1 offspring. We detected 202,349 high-quality SLAFs of which 144,972 were polymorphic; 10,042 SNPs were used to construct a genetic map that spanned 1,969.95 cM, with an average genetic distance of 0.23 cM between adjacent markers. This genetic map contains the largest molecular marker number of the grape maps so far reported. We thus demonstrate that SLAF-seq is a promising strategy for the construction of high-density genetic maps; the map that we report here is a good potential resource for QTL mapping of genes linked to major economic and agronomic traits, map-based cloning, and marker-assisted selection of grape.
Collapse
Affiliation(s)
- Jiahui Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
- * E-mail: (YSG); (XWG)
| | - Huiyang Xing
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Yuhui Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Zhendong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Kun Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Xiuwu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
- * E-mail: (YSG); (XWG)
| |
Collapse
|
29
|
Talukder SK, Saha MC. Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses. FRONTIERS IN PLANT SCIENCE 2017; 8:1317. [PMID: 28798766 PMCID: PMC5526908 DOI: 10.3389/fpls.2017.01317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 07/12/2017] [Indexed: 05/13/2023]
Abstract
Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind. In this review, we discuss the currently available genomics tools and approaches useful for C3 cool-season perennial grass breeding. Along with a general review, we emphasize the discussion focusing on forage grasses that were considered orphan and have little or no genetic information available. Transcriptome sequencing and genotype-by-sequencing technology for genome-wide marker detection using next-generation sequencing (NGS) are very promising as genomics tools. Most C3 cool-season perennial grass members have no prior genetic information; thus NGS technology will enhance collinear study with other C3 model grasses like Brachypodium and rice. Transcriptomics data can be used for identification of functional genes and molecular markers, i.e., polymorphism markers and simple sequence repeats (SSRs). Genome-wide association study with NGS-based markers will facilitate marker identification for marker-assisted selection. With limited genetic information, genomic selection holds great promise to breeders for attaining maximum genetic gain of the cool-season C3 perennial grasses. Application of all these tools can ensure better genetic gains, reduce length of selection cycles, and facilitate cultivar development to meet the future demand for food and fodder.
Collapse
|
30
|
Zhao Y, Su K, Wang G, Zhang L, Zhang J, Li J, Guo Y. High-Density Genetic Linkage Map Construction and Quantitative Trait Locus Mapping for Hawthorn (Crataegus pinnatifida Bunge). Sci Rep 2017; 7:5492. [PMID: 28710433 PMCID: PMC5511184 DOI: 10.1038/s41598-017-05756-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 06/14/2017] [Indexed: 11/30/2022] Open
Abstract
Genetic linkage maps are an important tool in genetic and genomic research. In this study, two hawthorn cultivars, Qiujinxing and Damianqiu, and 107 progenies from a cross between them were used for constructing a high-density genetic linkage map using the 2b-restriction site-associated DNA (2b-RAD) sequencing method, as well as for mapping quantitative trait loci (QTL) for flavonoid content. In total, 206,411,693 single-end reads were obtained, with an average sequencing depth of 57× in the parents and 23× in the progeny. After quality trimming, 117,896 high-quality 2b-RAD tags were retained, of which 42,279 were polymorphic; of these, 12,951 markers were used for constructing the genetic linkage map. The map contained 17 linkage groups and 3,894 markers, with a total map length of 1,551.97 cM and an average marker interval of 0.40 cM. QTL mapping identified 21 QTLs associated with flavonoid content in 10 linkage groups, which explained 16.30-59.00% of the variance. This is the first high-density linkage map for hawthorn, which will serve as a basis for fine-scale QTL mapping and marker-assisted selection of important traits in hawthorn germplasm and will facilitate chromosome assignment for hawthorn whole-genome assemblies in the future.
Collapse
Affiliation(s)
- Yuhui Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Gang Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Liping Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Jijun Zhang
- College of Horticulture Sciences & Technology, Hebei Normal University of Science & Technology, Qinhuangdao, China.
| | - Junpeng Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China.
| |
Collapse
|
31
|
Luo X, Xu L, Liang D, Wang Y, Zhang W, Zhu X, Zhu Y, Jiang H, Tang M, Liu L. Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.). BMC Genomics 2017; 18:505. [PMID: 28673249 PMCID: PMC5496183 DOI: 10.1186/s12864-017-3874-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 06/20/2017] [Indexed: 11/17/2022] Open
Abstract
Background Alternative splicing (AS) plays important roles in gene expression and proteome diversity. Single nucleotide polymorphism (SNP) and insertion/deletion (InDel) are abundant polymorphisms and co-dominant inheritance markers, which have been widely used in germplasm identification, genetic mapping and marker-assisted selection in plants. So far, however, little information is available on utilization of AS events and development of SNP and InDel markers from transcriptome in radish. Results In this study, three radish transcriptome datasets were collected and aligned to the reference radish genome. A total of 56,530 AS events were identified from three radish genotypes with intron retention (IR) being the most frequent AS type, which accounted for 59.4% of the total expressed genes in radish. In all, 22,412 SNPs and 9436 InDels were identified with an average frequency of 1 SNP/17.9 kb and 1 InDel/42.5 kb, respectively. A total of 43,680 potential SSRs were identified in 31,604 assembled unigenes with a density of 1 SSR/2.5 kb. The ratio of SNPs with nonsynonymous/synonymous mutations was 1.05:1. Moreover, 35 SNPs and 200 InDels were randomly selected and validated by Sanger sequencing, 83.9% of the SNPs and 70% of the InDels exhibited polymorphism among these three genotypes. In addition, the 15 SNPs and 125 InDels were found to be unevenly distributed on 9 linkage groups. Furthermore, 40 informative InDel markers were successfully used for the genetic diversity analysis on 32 radish accessions. Conclusions These results would not only provide new insights into transcriptome complexity and AS regulation, but also furnish large amount of molecular marker resources for germplasm identification, genetic mapping and further genetic improvement of radish in breeding programs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3874-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xiaobo Luo
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Dongyi Liang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Wei Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Yuelin Zhu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Haiyan Jiang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| |
Collapse
|
32
|
Wang J, Wang Z, Du X, Yang H, Han F, Han Y, Yuan F, Zhang L, Peng S, Guo E. A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq. PLoS One 2017. [PMID: 28644843 PMCID: PMC5482450 DOI: 10.1371/journal.pone.0179717] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Foxtail millet (Setaria italica), a very important grain crop in China, has become a new model plant for cereal crops and biofuel grasses. Although its reference genome sequence was released recently, quantitative trait loci (QTLs) controlling complex agronomic traits remains limited. The development of massively parallel genotyping methods and next-generation sequencing technologies provides an excellent opportunity for developing single-nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of complex quantitative traits. In this study, a high-throughput and cost-effective RAD-seq approach was employed to generate a high-density genetic map for foxtail millet. A total of 2,668,587 SNP loci were detected according to the reference genome sequence; meanwhile, 9,968 SNP markers were used to genotype 124 F2 progenies derived from the cross between Hongmiaozhangu and Changnong35; a high-density genetic map spanning 1648.8 cM, with an average distance of 0.17 cM between adjacent markers was constructed; 11 major QTLs for eight agronomic traits were identified; five co-dominant DNA markers were developed. These findings will be of value for the identification of candidate genes and marker-assisted selection in foxtail millet.
Collapse
Affiliation(s)
- Jun Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
- * E-mail: (JW); (EG)
| | - Zhilan Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Xiaofen Du
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Huiqing Yang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Fang Han
- Research Institute of Agriculture Sciences of Yanan, Yanan, Shaanxi, China
| | - Yuanhuai Han
- Shanxi Agricultural University, Taigu, Shanxi, China
| | - Feng Yuan
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Linyi Zhang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Shuzhong Peng
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Erhu Guo
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
- * E-mail: (JW); (EG)
| |
Collapse
|
33
|
Construction of a high-density linkage map and mapping of sex determination and growth-related loci in the mandarin fish (Siniperca chuatsi). BMC Genomics 2017; 18:446. [PMID: 28587594 PMCID: PMC5461734 DOI: 10.1186/s12864-017-3830-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 05/30/2017] [Indexed: 11/10/2022] Open
Abstract
Background The mandarin fish (Siniperca chuatsi) is an important and widely cultured fish in China. However, the lack of selective breeding of mandarin fish in previous decades has resulted in a decline in the growth rate of pond-cultured fish, a shortened period of sexual maturity, and reduced disease resistance; these issues seriously affect the quality and safety of the fish products. Therefore, it is necessary to establish a selective breeding program for the mandarin fish to improve the economical traits of the fish and to sustain the development of the mandarin fish industry. Results We constructed a high-density linkage map for it based on double digest restriction site associated DNA sequencing (ddRAD-Sequencing). This map contained 3283 dimorphic single nucleotide polymorphism markers and 24 linkage groups (LGs). The total map-length was 1972.01 cM, with an average interlocus distance of 0.61 cM. One significant quantitative trait locus (QTL) for sex determination trait was detected on LG23, which was supported by five markers, clustered between 60.27 and 68.71 cM. The highest logarithm of odds value (17.73) was located at 60.27 cM, near the marker r1_73194, accounting for 53.3% of the phenotypic variance. Genotypes of all the male fish on r1_33008 were homozygous, whereas those of all females were heterozygous. Thus, LG23 was considered a sex-related linkage group. Eleven significant QTLs, for three growth traits, at two growth stages and the increased values were distributed on four LGs; their contributions to the phenotypic variation were quite low (12.4–17.2%), suggesting that multiple genes affected the growth traits. Conclusion This high-resolution genetic map provides a valuable resource for fine-mapping of important traits and for identification of sex-related markers that should facilitate breeding of all-female mandarin fish for aquaculture and mechanistic studies on sex determination. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3830-3) contains supplementary material, which is available to authorized users.
Collapse
|
34
|
Footprints of domestication revealed by RAD-tag resequencing in loquat: SNP data reveals a non-significant domestication bottleneck and a single domestication event. BMC Genomics 2017; 18:354. [PMID: 28477616 PMCID: PMC5420408 DOI: 10.1186/s12864-017-3738-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/27/2017] [Indexed: 11/10/2022] Open
Abstract
Background The process of crop domestication has long been a major area of research to gain insights into the history of human civilization and to understand the process of evolution. Loquat (Eriobotrya japonica Lindl.) is one of the typical subtropical fruit trees, which was domesticated in China at least 2000 years ago. In the present study, we re-sequenced the genome of nine wild loquat accessions collected from wide geographical range and 10 representative cultivated loquat cultivars by using RAD-tag tacit to exploit the molecular footprints of domestication. Results We obtained 26.4 Gb clean sequencing data from 19 loquat accessions, with an average of 32.64 M reads per genotype. We identified more than 80,000 SNPs distributed throughout the loquat genome. The SNP density and numbers were slightly higher in the wild loquat populations than that in the cultivated populations. All cultivars were clustered together by structure, phylogenetic and PCA analyses. Conclusion The modern loquat cultivars have experienced a non-significant genetic bottleneck during domestication, and originated from a single domesticated event. Moreover, our study revealed that Hubei province of China is probably the origin center of cultivated loquat. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3738-y) contains supplementary material, which is available to authorized users.
Collapse
|
35
|
Ma B, Liao L, Peng Q, Fang T, Zhou H, Korban SS, Han Y. Reduced representation genome sequencing reveals patterns of genetic diversity and selection in apple. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:190-204. [PMID: 28093854 DOI: 10.1111/jipb.12522] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/15/2017] [Indexed: 05/02/2023]
Abstract
Identifying DNA sequence variations is a fundamental step towards deciphering the genetic basis of traits of interest. Here, a total of 20 cultivated and 10 wild apples were genotyped using specific-locus amplified fragment sequencing, and 39,635 single nucleotide polymorphisms with no missing genotypes and evenly distributed along the genome were selected to investigate patterns of genome-wide genetic variations between cultivated and wild apples. Overall, wild apples displayed higher levels of genetic diversity than cultivated apples. Linkage disequilibrium (LD) decays were observed quite rapidly in cultivated and wild apples, with an r2 -value below 0.2 at 440 and 280 bp, respectively. Moreover, bidirectional gene flow and different distribution patterns of LD blocks were detected between domesticated and wild apples. Most LD blocks unique to cultivated apples were located within QTL regions controlling fruit quality, thus suggesting that fruit quality had probably undergone selection during apple domestication. The genome of the earliest cultivated apple in China, Nai, was highly similar to that of Malus sieversii, and contained a small portion of genetic material from other wild apple species. This suggested that introgression could have been an important driving force during initial domestication of apple. These findings will facilitate future breeding and genetic dissection of complex traits in apple.
Collapse
Affiliation(s)
- Baiquan Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Liao Liao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Qian Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Ting Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Hui Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Schuyler S Korban
- Department of Biology, University of Massachusetts Boston, Boston Massachusetts 02184, USA
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| |
Collapse
|
36
|
Scheben A, Batley J, Edwards D. Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:149-161. [PMID: 27696619 PMCID: PMC5258866 DOI: 10.1111/pbi.12645] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/24/2016] [Accepted: 09/28/2016] [Indexed: 05/18/2023]
Abstract
In the last decade, the revolution in sequencing technologies has deeply impacted crop genotyping practice. New methods allowing rapid, high-throughput genotyping of entire crop populations have proliferated and opened the door to wider use of molecular tools in plant breeding. These new genotyping-by-sequencing (GBS) methods include over a dozen reduced-representation sequencing (RRS) approaches and at least four whole-genome resequencing (WGR) approaches. The diversity of methods available, each often producing different types of data at different cost, can make selection of the best-suited method seem a daunting task. We review the most common genotyping methods used today and compare their suitability for linkage mapping, genomewide association studies (GWAS), marker-assisted and genomic selection and genome assembly and improvement in crops with various genome sizes and complexity. Furthermore, we give an outline of bioinformatics tools for analysis of genotyping data. WGR is well suited to genotyping biparental cross populations with complex, small- to moderate-sized genomes and provides the lowest cost per marker data point. RRS approaches differ in their suitability for various tasks, but demonstrate similar costs per marker data point. These approaches are generally better suited for de novo applications and more cost-effective when genotyping populations with large genomes or high heterozygosity. We expect that although RRS approaches will remain the most cost-effective for some time, WGR will become more widespread for crop genotyping as sequencing costs continue to decrease.
Collapse
Affiliation(s)
- Armin Scheben
- School of Plant Biology and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - Jacqueline Batley
- School of Plant Biology and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - David Edwards
- School of Plant Biology and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| |
Collapse
|
37
|
Lowry DB, Hoban S, Kelley JL, Lotterhos KE, Reed LK, Antolin MF, Storfer A. Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation. Mol Ecol Resour 2016; 17:142-152. [PMID: 27860289 DOI: 10.1111/1755-0998.12635] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/23/2016] [Accepted: 09/02/2016] [Indexed: 12/26/2022]
Abstract
Understanding how and why populations evolve is of fundamental importance to molecular ecology. Restriction site-associated DNA sequencing (RADseq), a popular reduced representation method, has ushered in a new era of genome-scale research for assessing population structure, hybridization, demographic history, phylogeography and migration. RADseq has also been widely used to conduct genome scans to detect loci involved in adaptive divergence among natural populations. Here, we examine the capacity of those RADseq-based genome scan studies to detect loci involved in local adaptation. To understand what proportion of the genome is missed by RADseq studies, we developed a simple model using different numbers of RAD-tags, genome sizes and extents of linkage disequilibrium (length of haplotype blocks). Under the best-case modelling scenario, we found that RADseq using six- or eight-base pair cutting restriction enzymes would fail to sample many regions of the genome, especially for species with short linkage disequilibrium. We then surveyed recent studies that have used RADseq for genome scans and found that the median density of markers across these studies was 4.08 RAD-tag markers per megabase (one marker per 245 kb). The length of linkage disequilibrium for many species is one to three orders of magnitude less than density of the typical recent RADseq study. Thus, we conclude that genome scans based on RADseq data alone, while useful for studies of neutral genetic variation and genetic population structure, will likely miss many loci under selection in studies of local adaptation.
Collapse
Affiliation(s)
- David B Lowry
- Plant Biology Laboratories, Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Sean Hoban
- The Morton Arboretum, Lisle, IL, USA.,National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, TN, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, 430 Nahant Rd., Nahant, MA, 01908, USA
| | - Laura K Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35406, USA
| | - Michael F Antolin
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| |
Collapse
|
38
|
Bojahr J, Nhengiwa O, Krezdorn N, Rotter B, Saal B, Ruge-Wehling B, Struck C, Winter P. Massive analysis of cDNA ends (MACE) reveals a co-segregating candidate gene for LpPg1 stem rust resistance in perennial ryegrass (Lolium perenne). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1915-1932. [PMID: 27435735 DOI: 10.1007/s00122-016-2749-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/25/2016] [Indexed: 06/06/2023]
Abstract
Molecular markers including a potential resistance gene co-segregating with the LpPg1 stem rust resistance locus in perennial ryegrass were identified by massive analysis of cDNA ends (MACE) transcriptome profiling. Stem rust caused by Puccinia graminis subsp. graminicola is a severe fungal disease in the forage crop perennial ryegrass and other grasses. The previously identified LpPg1 locus confers efficient resistance against the pathogen. The aim of this study was to identify candidate genes involved in rust resistance and to use them as a resource for the development of molecular markers for LpPg1. To identify such candidates, bulked segregant analysis was combined with NGS-based massive analysis of cDNA ends (MACE) transcriptome profiling. Total RNA was isolated from bulks of infected and non-infected leaf segments from susceptible and resistant genotypes of a full-sibling mapping population and their respective parental lines and MACE was performed. Bioinformatic analysis detected 330 resistance-specific SNPs in 178 transcripts and 341 transcripts that were exclusively expressed in the resistant bulk. The sequences of many of these transcripts were homologous to genes in distinct regions of chromosomes one and four of the model grass Brachypodium distachyon. Of these, 30 were genetically mapped to a 50.8 cM spanning region surrounding the LpPg1 locus. One candidate NBS-LRR gene co-segregated with the resistance locus. Quantitative analysis of gene expression suggests that LpPg1 mediates an efficient resistance mechanism characterized by early recognition of the pathogen, fast defense signaling and rapid induction of antifungal proteins. We demonstrate here that MACE is a cost-efficient, fast and reliable tool that detects polymorphisms for genetic mapping of candidate resistance genes and simultaneously reveals deep insight into the molecular and genetic base of resistance.
Collapse
Affiliation(s)
- Jens Bojahr
- Group Crop Health, Faculty of Agricultural and Environmental Sciences, University of Rostock, Satower Str. 48, 18059, Rostock, Germany.
| | - Ottilia Nhengiwa
- Saatzucht Steinach GmbH & Co KG, Wittelsbacherstrasse 15, 94377, Steinach, Germany
| | - Nicolas Krezdorn
- GenXPro GmbH, Altenhöferallee 3, 60438, Frankfurt am Main, Germany
| | - Björn Rotter
- GenXPro GmbH, Altenhöferallee 3, 60438, Frankfurt am Main, Germany
| | - Bernhard Saal
- Saatzucht Steinach GmbH & Co KG, Wittelsbacherstrasse 15, 94377, Steinach, Germany
| | - Brigitte Ruge-Wehling
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, 18190, Sanitz, Germany
| | - Christine Struck
- Group Crop Health, Faculty of Agricultural and Environmental Sciences, University of Rostock, Satower Str. 48, 18059, Rostock, Germany
| | - Peter Winter
- GenXPro GmbH, Altenhöferallee 3, 60438, Frankfurt am Main, Germany
| |
Collapse
|
39
|
Jiang N, Zhang F, Wu J, Chen Y, Hu X, Fang O, Leach LJ, Wang D, Luo Z. A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1739-57. [PMID: 27316437 PMCID: PMC4983294 DOI: 10.1007/s00122-016-2736-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/28/2016] [Indexed: 05/14/2023]
Abstract
This optimized approach provides both a computational tool and a library construction protocol, which can maximize the number of genomic sequence reads that uniformly cover a plant genome and minimize the number of sequence reads representing chloroplast DNA and rRNA genes. One can implement the developed computational tool to feasibly design their own RAD-seq experiment to achieve expected coverage of sequence variant markers for large plant populations using information of the genome sequence and ideally, though not necessarily, information of the sequence polymorphism distribution in the genome. Advent of the next generation sequencing techniques motivates recent interest in developing sequence-based identification and genotyping of genome-wide genetic variants in large populations, with RAD-seq being a typical example. Without taking proper account for the fact that chloroplast and rRNA genes may occupy up to 60 % of the resulting sequence reads, the current RAD-seq design could be very inefficient for plant and crop species. We presented here a generic computational tool to optimize RAD-seq design in any plant species and experimentally tested the optimized design by implementing it to screen for and genotype sequence variants in four plant populations of diploid and autotetraploid Arabidopsis and potato Solanum tuberosum. Sequence data from the optimized RAD-seq experiments shows that the undesirable chloroplast and rRNA contributed sequence reads can be controlled at 3-10 %. Additionally, the optimized RAD-seq method enables pre-design of the required uniformity and density in coverage of the high quality sequence polymorphic markers over the genome of interest and genotyping of large plant or crop populations at a competitive cost in comparison to other mainstream rivals in the literature.
Collapse
Affiliation(s)
- Ning Jiang
- Department of Biostatistics and Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China
| | - Fengjun Zhang
- Department of Biostatistics and Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China
- Qinghai Academy of Agriculture and Forestry Sciences, Xining, Qinghai China
| | - Jinhua Wu
- Department of Biostatistics and Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China
| | - Yue Chen
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Xiaohua Hu
- Department of Biostatistics and Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China
| | - Ou Fang
- Department of Biostatistics and Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China
| | - Lindsey J. Leach
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Di Wang
- Gansu Agricultural University, Lanzhou, Gansu China
| | - Zewei Luo
- Department of Biostatistics and Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| |
Collapse
|
40
|
Mousavi M, Tong C, Liu F, Tao S, Wu J, Li H, Shi J. De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole-genome sequencing technologies. BMC Genomics 2016; 17:656. [PMID: 27538483 PMCID: PMC4991039 DOI: 10.1186/s12864-016-3003-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/09/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Restriction site associated DNA sequencing (RAD-seq), a next-generation sequencing technology, has greatly facilitated genetic linkage mapping studies in outbred species. RAD-seq is capable of discovering thousands of genetic markers for linkage mapping across many individuals, and can be applied in species with or without a reference genome. Although several analytical tools are available for RAD-seq data, alternative strategies are necessary for improving the marker quality and hence the genetic mapping accuracy. RESULTS We demonstrate a strategy for constructing dense genetic linkage maps in hybrid forest trees by combining RAD-seq and whole-genome sequencing technologies. We performed RAD-seq of 150 progeny and whole-genome sequencing of the two parents in an F1 hybrid population of Populus deltoides × P. simonii. Two rough references were assembled from the whole-genome sequencing reads of the two parents separately. Based on the parental reference sequences, 3442 high-quality single nucleotide polymorphisms (SNPs) were identified that segregate in the ratio of 1:1. The maternal linkage map of P. deltoides was constructed with 2012 SNPs, containing 19 linkage groups and spanning 4067.16 cM of the genome with an average distance of 2.04 cM between adjacent markers, while the male map of P. simonii consisted of 1430 SNPs and the same number of linkage groups with a total length of 4356.04 cM and an average interval distance of 3.09 cM. Collinearity between the parental linkage maps and the reference genome of P. trichocarpa was also investigated. Compared with the result on the basis of the existing reference genome, our strategy identified more high-quality SNPs and generated parental linkage groups that nicely match the karyotype of Populus. CONCLUSIONS The strategy of simultaneously using RAD and whole-genome sequencing technologies can be applied to constructing high-density genetic maps in forest trees regardless of whether a reference genome exists. The two parental linkage maps constructed here provide more accurate genetic resources for unraveling quantitative trait loci and accelerating molecular breeding programs, as well as for comparative genomics in Populus.
Collapse
Affiliation(s)
- Mohaddeseh Mousavi
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Chunfa Tong
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Fenxiang Liu
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Shentong Tao
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Jiyan Wu
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Huogen Li
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Jisen Shi
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| |
Collapse
|
41
|
Huang X, Wang F, Singh R, Reinert JA, Engelke MC, Genovesi AD, Chandra A, Yu Q. Construction of high-resolution genetic maps of Zoysia matrella (L.) Merrill and applications to comparative genomic analysis and QTL mapping of resistance to fall armyworm. BMC Genomics 2016; 17:562. [PMID: 27501690 PMCID: PMC4977732 DOI: 10.1186/s12864-016-2969-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/26/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Zoysia matrella, widely used in lawns and sports fields, is of great economic and ecological value. Z. matrella is an allotetraploid species (2n = 4x = 40) in the genus zoysia under the subfamily Chloridoideae. Despite its ecological impacts and economic importance, the subfamily Chloridoideae has received little attention in genomics studies. As a result, limited genetic and genomic information are available for this subfamily, which have impeded progress in understanding evolutionary history of grasses in this important lineage. The lack of a high-resolution genetic map has hampered efforts to improve zoysiagrass using molecular genetic tools. RESULTS We used restriction site-associated DNA sequencing (RADSeq) approach and a segregating population developed from the cross between Z. matrella cultivars 'Diamond' and 'Cavalier' to construct high-resolution genetic maps of Z. matrella. The genetic map of Diamond consists of 2,375 Single Nucleotide Polymorphism (SNP) markers mapped on 20 linkage groups (LGs) with a total length of 1754.48 cM and an average distance between adjacent markers at 0.74 cM. The genetic map of Cavalier contains 3,563 SNP markers on 20 LGs, covering 1824.92 cM, with an average distance between adjacent markers at 0.51 cM. A higher level of genome collinearity between Z. matrella and rice than that between Z. matrella and sorghum was revealed by comparative genomic analysis. Pairwise comparison revealed that two independent nested chromosome fusion events occurred after Z. matrella and sorghum split from a common ancestor. The high-resolution linkage maps were applied into mapping QTLs associated with fall armyworm (FAW) resistance and six loci located on LGs 8 and 20 were detected to be significantly associated with FAW resistance. CONCLUSION The high-resolution linkage maps provide anchor points for comparative genomics analysis between Z. matrella and other grass species. Our comparative genomic analysis suggested that the chromosome number reduction from 12 to 10 had occurred independently via a single-step in the subfamilies Chloridoideae and Panicoideae. The high-resolution genetic maps provide an essential framework for mapping QTLs associated with economically and agronomically important traits. The major QTLs mapped on LG8 of the Cavalier map provide a starting point for cloning FAW resistance genes and further studies for a better understanding of FAW resistance in zoysiagrass.
Collapse
Affiliation(s)
- Xiaoen Huang
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX 75252 USA
| | - Fangfang Wang
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX 75252 USA
| | - Ratnesh Singh
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX 75252 USA
| | - James A. Reinert
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX 75252 USA
| | - M. C. Engelke
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX 75252 USA
| | - Anthony D. Genovesi
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX 75252 USA
| | - Ambika Chandra
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX 75252 USA
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Qingyi Yu
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX 75252 USA
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77843 USA
| |
Collapse
|
42
|
Onda Y, Mochida K. Exploring Genetic Diversity in Plants Using High-Throughput Sequencing Techniques. Curr Genomics 2016; 17:358-67. [PMID: 27499684 PMCID: PMC4955029 DOI: 10.2174/1389202917666160331202742] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 07/19/2015] [Accepted: 07/21/2015] [Indexed: 12/31/2022] Open
Abstract
Food security has emerged as an urgent concern because of the rising world population. To meet the food demands of the near future, it is required to improve the productivity of various crops, not just of staple food crops. The genetic diversity among plant populations in a given species allows the plants to adapt to various environmental conditions. Such diversity could therefore yield valuable traits that could overcome the food-security challenges. To explore genetic diversity comprehensively and to rapidly identify useful genes and/or allele, advanced high-throughput sequencing techniques, also called next-generation sequencing (NGS) technologies, have been developed. These provide practical solutions to the challenges in crop genomics. Here, we review various sources of genetic diversity in plants, newly developed genetic diversity-mining tools synergized with NGS techniques, and related genetic approaches such as quantitative trait locus analysis and genome-wide association study.
Collapse
Affiliation(s)
- Yoshihiko Onda
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa,Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa,Japan
| | - Keiichi Mochida
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa,Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa,Japan
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Kanagawa,Japan
| |
Collapse
|
43
|
Wang J, Sun G, Ren X, Li C, Liu L, Wang Q, Du B, Sun D. QTL underlying some agronomic traits in barley detected by SNP markers. BMC Genet 2016; 17:103. [PMID: 27388211 PMCID: PMC4936321 DOI: 10.1186/s12863-016-0409-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/24/2016] [Indexed: 12/30/2022] Open
Abstract
Background Increasing the yield of barley (Hordeum vulgare L.) is a main breeding goal in developing barley cultivars. A high density genetic linkage map containing 1894 SNP and 68 SSR markers covering 1375.8 cM was constructed and used for mapping quantitative traits. A late-generation double haploid population (DH) derived from the Huaai 11 × Huadamai 6 cross was used to identify QTLs and QTL × environment interactions for ten traits affecting grain yield including length of main spike (MSL), spikelet number on main spike (SMS), spikelet number per plant (SLP), grain number per plant (GP), grain weight per plant (GWP), grain number per spike (GS), thousand grain weight (TGW), grain weight per spike (GWS), spike density (SPD) and spike number per plant (SP). Results In single environment analysis using composite interval mapping (CIM), a total of 221 QTLs underlying the ten traits were detected in five consecutive years (2009–2013). The QTLs detected in each year were 50, 48, 41, 41 and 41 for the year 2009 to 2013. The QTLs associated with these traits were generally clustered on chromosome 2H, 4H and 7H. In multi-environment analysis, a total of 111 significant QTLs including 18 for MSL, 16 for SMS, 15 for SPD, 5 for SP, 4 for SLP, 14 for TGW, 5 for GP, 11 for GS, 8 for GWP, and 15 for GWS were detected in the five years. Most QTLs showed significant QTL × environment interactions (QEI), nine QTLs (qIMSL3-1, qIMSL4-1, qIMSL4-2, qIMSL6-1, qISMS7-1, qISPD2-7, qISPD7-1, qITGW3-1 and qIGWS4-3) were detected with minimal QEI effects and stable in different years. Among 111 QTLs,71 (63.40 %) QTLs were detected in both single and multiple environments. Conclusions Three main QTL cluster regions associated with the 10 agronomic traits on chromosome 2H, 4H and 7H were detected. The QTLs for SMS, SLP, GP and GWP were located in the region near Vrs1 on chromosome 2H. The QTLs underlying SMS, SPD and SLP were clustered on chromosome 4H. On the terminal of chromosome 7H, there was a QTL cluster associated with TGW, SPD, GWP and GWS. The information will be useful for marker-assisted selection (MAS) in barley breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0409-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jibin Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Genlou Sun
- Biology Department, Saint Mary's University, 923 Robie Street, Halifax, NS, B3H 3C3, Canada
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chengdao Li
- Department of Agriculture & Food/Agricultural Research Western Australia, 3 Baron-Hay Court, South Perth, WA, 6155, Australia
| | - Lipan Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qifei Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Binbin Du
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, 434025, Hubei, China.
| |
Collapse
|
44
|
Quantitative trait locus analysis of body shape divergence in nine-spined sticklebacks based on high-density SNP-panel. Sci Rep 2016; 6:26632. [PMID: 27226078 PMCID: PMC4880927 DOI: 10.1038/srep26632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 05/06/2016] [Indexed: 12/26/2022] Open
Abstract
Heritable phenotypic differences between populations, caused by the selective effects of distinct environmental conditions, are of commonplace occurrence in nature. However, the actual genomic targets of this kind of selection are still poorly understood. We conducted a quantitative trait locus (QTL) mapping study to identify genomic regions responsible for morphometric differentiation between genetically and phenotypically divergent marine and freshwater nine-spined stickleback (Pungitius pungitius) populations. Using a dense panel of SNP-markers obtained by restriction site associated DNA sequencing of an F2 recombinant cross, we found 22 QTL that explained 3.5-12.9% of phenotypic variance in the traits under investigation. We detected one fairly large-effect (PVE = 9.6%) QTL for caudal peduncle length-a trait with a well-established adaptive function showing clear differentiation among marine and freshwater populations. We also identified two large-effect QTL for lateral plate numbers, which are different from the lateral plate QTL reported in earlier studies of this and related species. Hence, apart from identifying several large-effect QTL in shape traits showing adaptive differentiation in response to different environmental conditions, the results suggest intra- and interspecific heterogeneity in the genomic basis of lateral plate number variation.
Collapse
|
45
|
Yu F, Zhang X, Huang Z, Chu M, Song T, Falk KC, Deora A, Chen Q, Zhang Y, McGregor L, Gossen BD, McDonald MR, Peng G. Identification of Genome-Wide Variants and Discovery of Variants Associated with Brassica rapa Clubroot Resistance Gene Rcr1 through Bulked Segregant RNA Sequencing. PLoS One 2016; 11:e0153218. [PMID: 27078023 DOI: 10.1371/journal.pone.00153218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/27/2016] [Indexed: 05/26/2023] Open
Abstract
Clubroot, caused by Plasmodiophora brassicae, is an important disease on Brassica species worldwide. A clubroot resistance gene, Rcr1, with efficacy against pathotype 3 of P. brassicae, was previously mapped to chromosome A03 of B. rapa in pak choy cultivar "Flower Nabana". In the current study, resistance to pathotypes 2, 5 and 6 was shown to be associated with Rcr1 region on chromosome A03. Bulked segregant RNA sequencing was performed and short read sequences were assembled into 10 chromosomes of the B. rapa reference genome v1.5. For the resistant (R) bulks, a total of 351.8 million (M) sequences, 30,836.5 million bases (Mb) in length, produced 120-fold coverage of the reference genome. For the susceptible (S) bulks, 322.9 M sequences, 28,216.6 Mb in length, produced 109-fold coverage. In total, 776.2 K single nucleotide polymorphisms (SNPs) and 122.2 K insertion / deletion (InDels) in R bulks and 762.8 K SNPs and 118.7 K InDels in S bulks were identified; each chromosome had about 87% SNPs and 13% InDels, with 78% monomorphic and 22% polymorphic variants between the R and S bulks. Polymorphic variants on each chromosome were usually below 23%, but made up 34% of the variants on chromosome A03. There were 35 genes annotated in the Rcr1 target region and variants were identified in 21 genes. The numbers of poly variants differed significantly among the genes. Four out of them encode Toll-Interleukin-1 receptor / nucleotide-binding site / leucine-rich-repeat proteins; Bra019409 and Bra019410 harbored the higher numbers of polymorphic variants, which indicates that they are more likely candidates of Rcr1. Fourteen SNP markers in the target region were genotyped using the Kompetitive Allele Specific PCR method and were confirmed to associate with Rcr1. Selected SNP markers were analyzed with 26 recombinants obtained from a segregating population consisting of 1587 plants, indicating that they were completely linked to Rcr1. Nine SNP markers were used for marker-assisted introgression of Rcr1 into B. napus canola from B. rapa, with 100% accuracy in this study.
Collapse
Affiliation(s)
- Fengqun Yu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Xingguo Zhang
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Zhen Huang
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Mingguang Chu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Tao Song
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Kevin C Falk
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Abhinandan Deora
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
| | - Qilin Chen
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Yan Zhang
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Linda McGregor
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Bruce D Gossen
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Mary Ruth McDonald
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
| | - Gary Peng
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| |
Collapse
|
46
|
Identification of Genome-Wide Variants and Discovery of Variants Associated with Brassica rapa Clubroot Resistance Gene Rcr1 through Bulked Segregant RNA Sequencing. PLoS One 2016; 11:e0153218. [PMID: 27078023 PMCID: PMC4831815 DOI: 10.1371/journal.pone.0153218] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/27/2016] [Indexed: 11/19/2022] Open
Abstract
Clubroot, caused by Plasmodiophora brassicae, is an important disease on Brassica species worldwide. A clubroot resistance gene, Rcr1, with efficacy against pathotype 3 of P. brassicae, was previously mapped to chromosome A03 of B. rapa in pak choy cultivar “Flower Nabana”. In the current study, resistance to pathotypes 2, 5 and 6 was shown to be associated with Rcr1 region on chromosome A03. Bulked segregant RNA sequencing was performed and short read sequences were assembled into 10 chromosomes of the B. rapa reference genome v1.5. For the resistant (R) bulks, a total of 351.8 million (M) sequences, 30,836.5 million bases (Mb) in length, produced 120-fold coverage of the reference genome. For the susceptible (S) bulks, 322.9 M sequences, 28,216.6 Mb in length, produced 109-fold coverage. In total, 776.2 K single nucleotide polymorphisms (SNPs) and 122.2 K insertion / deletion (InDels) in R bulks and 762.8 K SNPs and 118.7 K InDels in S bulks were identified; each chromosome had about 87% SNPs and 13% InDels, with 78% monomorphic and 22% polymorphic variants between the R and S bulks. Polymorphic variants on each chromosome were usually below 23%, but made up 34% of the variants on chromosome A03. There were 35 genes annotated in the Rcr1 target region and variants were identified in 21 genes. The numbers of poly variants differed significantly among the genes. Four out of them encode Toll-Interleukin-1 receptor / nucleotide-binding site / leucine-rich-repeat proteins; Bra019409 and Bra019410 harbored the higher numbers of polymorphic variants, which indicates that they are more likely candidates of Rcr1. Fourteen SNP markers in the target region were genotyped using the Kompetitive Allele Specific PCR method and were confirmed to associate with Rcr1. Selected SNP markers were analyzed with 26 recombinants obtained from a segregating population consisting of 1587 plants, indicating that they were completely linked to Rcr1. Nine SNP markers were used for marker-assisted introgression of Rcr1 into B. napus canola from B. rapa, with 100% accuracy in this study.
Collapse
|
47
|
Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing. PLoS One 2016; 11:e0150692. [PMID: 26964097 PMCID: PMC4786213 DOI: 10.1371/journal.pone.0150692] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 02/18/2016] [Indexed: 11/19/2022] Open
Abstract
Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides 'I-69' and male Populus simonii 'L3'. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population.
Collapse
|
48
|
Boutet G, Alves Carvalho S, Falque M, Peterlongo P, Lhuillier E, Bouchez O, Lavaud C, Pilet-Nayel ML, Rivière N, Baranger A. SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population. BMC Genomics 2016; 17:121. [PMID: 26892170 PMCID: PMC4758021 DOI: 10.1186/s12864-016-2447-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/08/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Progress in genetics and breeding in pea still suffers from the limited availability of molecular resources. SNP markers that can be identified through affordable sequencing processes, without the need for prior genome reduction or a reference genome to assemble sequencing data would allow the discovery and genetic mapping of thousands of molecular markers. Such an approach could significantly speed up genetic studies and marker assisted breeding for non-model species. RESULTS A total of 419,024 SNPs were discovered using HiSeq whole genome sequencing of four pea lines, followed by direct identification of SNP markers without assembly using the discoSnp tool. Subsequent filtering led to the identification of 131,850 highly designable SNPs, polymorphic between at least two of the four pea lines. A subset of 64,754 SNPs was called and genotyped by short read sequencing on a subpopulation of 48 RILs from the cross 'Baccara' x 'PI180693'. This data was used to construct a WGGBS-derived pea genetic map comprising 64,263 markers. This map is collinear with previous pea consensus maps and therefore with the Medicago truncatula genome. Sequencing of four additional pea lines showed that 33 % to 64 % of the mapped SNPs, depending on the pairs of lines considered, are polymorphic and can therefore be useful in other crosses. The subsequent genotyping of a subset of 1000 SNPs, chosen for their mapping positions using a KASP™ assay, showed that almost all generated SNPs are highly designable and that most (95 %) deliver highly qualitative genotyping results. Using rather low sequencing coverages in SNP discovery and in SNP inferring did not hinder the identification of hundreds of thousands of high quality SNPs. CONCLUSIONS The development and optimization of appropriate tools in SNP discovery and genetic mapping have allowed us to make available a massive new genomic resource in pea. It will be useful for both fine mapping within chosen QTL confidence intervals and marker assisted breeding for important traits in pea improvement.
Collapse
Affiliation(s)
- Gilles Boutet
- INRA, UMR 1349 IGEPP, BP35327, Le Rheu Cedex, 35653, France.
- PISOM, UMT INRA/CETIOM, BP35327, Le Rheu Cedex, 35653, France.
| | - Susete Alves Carvalho
- INRA, UMR 1349 IGEPP, BP35327, Le Rheu Cedex, 35653, France.
- INRIA Rennes - Bretagne Atlantique/IRISA, EPI GenScale, Rennes, 35042, France.
| | - Matthieu Falque
- INRA, UMR Génétique Quantitative et Evolution - Le Moulon, INRA - Univ Paris-Sud - CNRS - AgroParisTech, Ferme du Moulon, 91190, Gif-sur-Yvette, France.
| | - Pierre Peterlongo
- INRIA Rennes - Bretagne Atlantique/IRISA, EPI GenScale, Rennes, 35042, France.
| | - Emeline Lhuillier
- GeT-PlaGe, Genotoul, INRA Auzeville F31326, Castanet-tolosan, France.
| | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRA Auzeville F31326, Castanet-tolosan, France.
- INRA, UMR1388 INRA/ENVT/ENSAT GenPhySE, INRA Auzeville F31326, Castanet-tolosan, France.
| | - Clément Lavaud
- INRA, UMR 1349 IGEPP, BP35327, Le Rheu Cedex, 35653, France.
- PISOM, UMT INRA/CETIOM, BP35327, Le Rheu Cedex, 35653, France.
| | - Marie-Laure Pilet-Nayel
- INRA, UMR 1349 IGEPP, BP35327, Le Rheu Cedex, 35653, France.
- PISOM, UMT INRA/CETIOM, BP35327, Le Rheu Cedex, 35653, France.
| | | | - Alain Baranger
- INRA, UMR 1349 IGEPP, BP35327, Le Rheu Cedex, 35653, France.
- PISOM, UMT INRA/CETIOM, BP35327, Le Rheu Cedex, 35653, France.
| |
Collapse
|
49
|
Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding. PLoS One 2016; 11:e0147187. [PMID: 26799713 PMCID: PMC4723255 DOI: 10.1371/journal.pone.0147187] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 12/30/2015] [Indexed: 11/19/2022] Open
Abstract
Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genome-wide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection.
Collapse
|
50
|
Jiang B, Liu W, Xie D, Peng Q, He X, Lin Y, Liang Z. High-density genetic map construction and gene mapping of pericarp color in wax gourd using specific-locus amplified fragment (SLAF) sequencing. BMC Genomics 2015; 16:1035. [PMID: 26647294 PMCID: PMC4673774 DOI: 10.1186/s12864-015-2220-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/16/2015] [Indexed: 11/10/2022] Open
Abstract
Background High-density map is a valuable tool for genetic and genomic analysis. Although wax gourd is a widely distributed vegetable of Cucurbitaceae and has important medicinal and health value, no genetic map has been constructed because of the lack of efficient markers. Specific-locus amplified fragment sequencing (SLAF-seq) is a newly developed high-throughput strategy for large-scale single nucleotide polymorphism (SNP) discovery and genotyping. Results In our present study, we constructed a high-density genetic map by using SLAF-seq and identified a locus controlling pericarp color in wax gourd. An F2 population of 140 individuals and their two parents were subjected to SLAF-seq. A total of 143.38 M pair-end reads were generated. The average sequencing depth was 26.51 in the maternal line (B214), 27.01 in the parental line (B227), and 5.11 in each F2 individual. When filtering low-depth SLAF tags, a total of 142,653 high-quality SLAFs were detected, and 22,151 of them were polymorphic, with a polymorphism rate of 15.42 %. And finally, 4,607 of the polymorphic markers were selected for genetic map construction, and 12 linkage groups (LGs) were generated. The map spanned 2,172.86 cM with an average distance between adjacent markers for 0.49 cM. The inheritance of pericarp color was also studied, which showed that the pericarp color was controlled by one single gene. And based on the newly constructed high-density map, a single locus locating on chromosome 5 was identified for controlling the pericarp color of wax gourd. Conclusions This is the first report of high-density genetic map construction and gene mapping in wax gourd, which will be served as an invaluable tool for gene mapping, marker assisted breeding, map-based gene cloning, comparative mapping and draft genome assembling of wax gourd. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2220-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China
| | - Wenrui Liu
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China
| | - Dasen Xie
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China. .,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China.
| | - Qingwu Peng
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China
| | - Xiaoming He
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China
| | - Yu'e Lin
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China
| | - Zhaojun Liang
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China
| |
Collapse
|