1
|
Chen X, Peng M, Yang C, Li Q, Feng P, Zhu W, Zhang Y, Zeng D, Zhao Y. Genome-wide QTL and eQTL mapping reveal genes associated with growth rate trait of the Pacific white shrimp (Litopenaeus vannamei). BMC Genomics 2024; 25:414. [PMID: 38671371 PMCID: PMC11046935 DOI: 10.1186/s12864-024-10328-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Growth rate is a crucial economic trait for farmed animals, but the genetic regulation of this trait is largely unknown in non-model organisms such as shrimp. RESULTS In this study, we performed genome-wide phenotypic quantitative trait loci (QTL) and expression quantitative trait loci (eQTL) mapping analyses to identify genes affecting the growth rate of Pacific white shrimp (Litopenaeus vannamei), which is the most commercially-farmed crustacean worldwide. We used RNA-sequencing of 268 individuals in a mapping population, and subsequently validated our findings through gene silencing and shrimp growth experiments. We constructed a high-density genetic linkage map comprising 5533 markers spanning 44 linkage groups, with a total distance of 6205.75 cM and an average marker interval of 1.12 cM. Our analyses identified 11 QTLs significantly correlated with growth rate, and 117,525 eQTLs. By integrating QTL and eQTL data, we identified a gene (metalloreductase STEAP4) highly associated with shrimp growth rate. RNA interference (RNAi) analysis and growth experiments confirmed that STEAP4 was significantly correlated with growth rate in L. vannamei. CONCLUSIONS Our results indicate that the comprehensive analysis of QTL and eQTL can effectively identify genes involved in complex animal traits. This is important for marker-assisted selection (MAS) of animals. Our work contributes to the development of shrimp breeding and available genetic resources.
Collapse
Affiliation(s)
- Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Chunling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Qiangyong Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Pengfei Feng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Weilin Zhu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Yongde Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Digang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
| |
Collapse
|
2
|
Poonam, Sharma R, Sharma P, Sharma NC, Kumar K, Singh KN, Bhardwaj V, Negi N, Chauhan N. Exploring genetic diversity and ascertaining genetic loci associated with important fruit quality traits in apple ( Malus × domestica Borkh.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1693-1716. [PMID: 38162921 PMCID: PMC10754789 DOI: 10.1007/s12298-023-01382-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
Genetic diversity is the primary source of variability in any crop improvement program, and the diverse germplasm of any crop species represents an important genetic resource for gene or allele mining to meet future needs. Huge genetic and phenotypic diversity is present in the apple gene pool, even though, breeding programs have been mainly focused on a few traits of interests, which have resulted in the reduction of the diversity in the cultivated lines of apple. Therefore, the present study was carried out on 70 diverse apple genotypes with the objective of analyzing the genetic diversity and to identify the genetic loci associated with important fruit quality traits. A total of 140 SSR primers were used to characterize the 70 genotypes of apples, out of which only 88 SSRs were found to be polymorphic. The PIC values varied from 0.03 to 0.75. The value of MI, EMR, and RP varied from 0.03 to 3.5, 0.5 to 5.0, and 1.89 to 6.74, respectively. The dendrogram and structure analysis divided all the genotypes into two main groups. In addition to this, large phenotypic variability was observed for the fruit quality traits under study indicated the suitability of the genotypes for association studies. Altogether 71 novel MTAs were identified for 10 fruit quality traits, of which 15 for fruit length, 15 for fruit diameter, 12 for fruit weight, 2 for total sugar, 2 for TSS, 4 for reducing sugar, 5 for non-reducing sugar, 5 for fruit firmness, 5 for fruit acidity and 6 for anthocyanin, respectively. Consistent with the physicochemical evaluation of traits, there was a significant correlation coefficient among different fruit quality characters, and many common markers were found to be associated with these traits (fruit diameter, length, TSS, total sugar, acidity and anthocyanin, respectively) by using the different modeling techniques (GLM, MLM). The inferred genetic structure, diversity pattern and the identified MTAs will be serving as resourceful grounds for better predictions and understanding of apple genome towards efficient conservation and utilization of apple germplasm for facilitating genetic improvement of fruit quality traits. Furthermore, these findings also suggested that association mapping could be a viable alternative to the conventional QTL mapping approach in apple. Graphic abstract Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01382-w.
Collapse
Affiliation(s)
- Poonam
- Department of Biotechnology, Dr YS Parmar University of Horticulture & Forestry, Solan, HP 173 230 India
- School of Bioengineering & Food Technology, Shoolini University, Solan, HP, 173 229, India
| | - Rajnish Sharma
- Department of Biotechnology, Dr YS Parmar University of Horticulture & Forestry, Solan, HP 173 230 India
| | - Parul Sharma
- Department of Biotechnology, Dr YS Parmar University of Horticulture & Forestry, Solan, HP 173 230 India
| | - Naveen C. Sharma
- Department of Fruit Science, Dr YS Parmar University of Horticulture & Forestry, Solan, HP 173 230 India
| | - Kuldeep Kumar
- ICAR-Indian Institute of Pulses Research, Kanpur, UP 208 024 India
| | - Krishna Nand Singh
- Department of Botany, University of Delhi, North Campus, New Delhi, India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, HP 171 004 India
| | - Narender Negi
- ICAR-NBPGR Regional Station, Phagli, Shimla, HP 171 004 India
| | - Neena Chauhan
- RHR&TS, Dr YS Parmar University of Horticulture & Forestry, Mashobra, Shimla, HP, 171 007 India
| |
Collapse
|
3
|
Wei J, Chen Y, Wang W. A High-Density Genetic Linkage Map and QTL Mapping for Sex and Growth-Related Traits of Large-Scale Loach ( Paramisgurnus dabryanus). Front Genet 2019; 10:1023. [PMID: 31708968 PMCID: PMC6823184 DOI: 10.3389/fgene.2019.01023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/24/2019] [Indexed: 12/30/2022] Open
Abstract
Large-scale loach (Paramisgurnus dabryanus) is a commercially important species in East Asia; however, the cultured population that exhibited degradation of germplasm resource cannot meet the market needs, and the genome resources for P. dabryanus are still lacking. In this study, the first high-density genetic map of P. dabryanus was constructed using 15,830 SNP markers based on high-throughput sequencing with an improved SLAF-seq strategy. The quantitative trait locus (QTL) mapping for sex, growth, and morphology traits was performed for the first time. The genetic map spanned 4,657.64 cM in length with an average inter-marker distance of 0.30 cM. QTL mapping and association analysis identified eight QTLs of growth traits, nine QTLs of morphology traits, and five QTLs of sex-related traits, respectively. Interestingly, the most significant QTLs for almost all the traits were concentrated on the same linkage group LG11. Seven candidate markers and 12 potentially key genes, which were associated with sex determination and growth, were identified within the overlapped QTL regions on LG11. Further, the first genome survey analysis of P. dabryanus was performed which represents the first step toward fully decoding the P. dabryanus genome. The genome scaffolds were anchored to the high-density linkage map, spanning 960.27 Mb of P. dabryanus reference genome. The collinearity analysis revealed a high level of collinearity between the genetic map and the reference genome of P. dabryanus. Moreover, a certain degree of homology was observed between large-scale loach and zebrafish using comparative genomic analysis. The constructed high-density genetic map was an important basis for QTL fine mapping, genome assembly, and genome comparison. The present study will provide a valuable resource for future marker-assisted breeding, and further genetic and genomic researches in P. dabryanus.
Collapse
Affiliation(s)
- Jin Wei
- Key Lab of Agricultural Animal Genetics, College of Fisheries, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Yuanyuan Chen
- Key Lab of Agricultural Animal Genetics, College of Fisheries, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Weimin Wang
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
4
|
Norelli JL, Wisniewski M, Fazio G, Burchard E, Gutierrez B, Levin E, Droby S. Genotyping-by-sequencing markers facilitate the identification of quantitative trait loci controlling resistance to Penicillium expansum in Malus sieversii. PLoS One 2017; 12:e0172949. [PMID: 28257442 PMCID: PMC5336245 DOI: 10.1371/journal.pone.0172949] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/13/2017] [Indexed: 11/30/2022] Open
Abstract
Blue mold caused by Penicillium expansum is the most important postharvest disease of apple worldwide and results in significant financial losses. There are no defined sources of resistance to blue mold in domesticated apple. However, resistance has been described in wild Malus sieversii accessions, including plant introduction (PI)613981. The objective of the present study was to identify the genetic loci controlling resistance to blue mold in this accession. We describe the first quantitative trait loci (QTL) reported in the Rosaceae tribe Maleae conditioning resistance to P. expansum on genetic linkage group 3 (qM-Pe3.1) and linkage group 10 (qM-Pe10.1). These loci were identified in a M.× domestica 'Royal Gala' X M. sieversii PI613981 family (GMAL4593) based on blue mold lesion diameter seven days post-inoculation in mature, wounded apple fruit inoculated with P. expansum. Phenotypic analyses were conducted in 169 progeny over a four year period. PI613981 was the source of the resistance allele for qM-Pe3.1, a QTL with a major effect on blue mold resistance, accounting for 27.5% of the experimental variability. The QTL mapped from 67.3 to 74 cM on linkage group 3 of the GMAL4593 genetic linkage map. qM-Pe10.1 mapped from 73.6 to 81.8 cM on linkage group 10. It had less of an effect on resistance, accounting for 14% of the experimental variation. 'Royal Gala' was the primary contributor to the resistance effect of this QTL. However, resistance-associated alleles in both parents appeared to contribute to the least square mean blue mold lesion diameter in an additive manner at qM-Pe10.1. A GMAL4593 genetic linkage map composed of simple sequence repeats and 'Golden Delicious' single nucleotide polymorphism markers was able to detect qM-Pe10.1, but failed to detect qM-Pe3.1. The subsequent addition of genotyping-by-sequencing markers to the linkage map provided better coverage of the PI613981 genome on linkage group 3 and facilitated discovery of qM-Pe3.1. A DNA test for qM-Pe3.1 has been developed and is currently being evaluated for its ability to predict blue mold resistance in progeny segregating for qM-Pe3.1. Due to the long juvenility of apple, the availability of a DNA test to screen for the presence of qM-Pe3.1 at the seedling stage will greatly improve efficiency of breeding apple for blue mold resistance.
Collapse
Affiliation(s)
- John L. Norelli
- Appalachian Fruit Research Station, Agricultural Research Service, United States Department of Agriculture, Kearneysville, West Virginia, United States of America
| | - Michael Wisniewski
- Appalachian Fruit Research Station, Agricultural Research Service, United States Department of Agriculture, Kearneysville, West Virginia, United States of America
| | - Gennaro Fazio
- Plant Genetic Resources Research, Agricultural Research Service, United States Department of Agriculture, Geneva, New York, United States of America
| | - Erik Burchard
- Appalachian Fruit Research Station, Agricultural Research Service, United States Department of Agriculture, Kearneysville, West Virginia, United States of America
| | - Benjamin Gutierrez
- Plant Genetic Resources Research, Agricultural Research Service, United States Department of Agriculture, Geneva, New York, United States of America
| | - Elena Levin
- Department of Postharvest Science, Agricultural Research Organization, the Volcani Center, Bet Dagan, Israel
| | - Samir Droby
- Department of Postharvest Science, Agricultural Research Organization, the Volcani Center, Bet Dagan, Israel
| |
Collapse
|
5
|
Di Pierro EA, Gianfranceschi L, Di Guardo M, Koehorst-van Putten HJJ, Kruisselbrink JW, Longhi S, Troggio M, Bianco L, Muranty H, Pagliarani G, Tartarini S, Letschka T, Lozano Luis L, Garkava-Gustavsson L, Micheletti D, Bink MCAM, Voorrips RE, Aziz E, Velasco R, Laurens F, van de Weg WE. A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species. HORTICULTURE RESEARCH 2016; 3:16057. [PMID: 27917289 PMCID: PMC5120355 DOI: 10.1038/hortres.2016.57] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 10/25/2016] [Accepted: 10/25/2016] [Indexed: 05/18/2023]
Abstract
Quantitative trait loci (QTL) mapping approaches rely on the correct ordering of molecular markers along the chromosomes, which can be obtained from genetic linkage maps or a reference genome sequence. For apple (Malus domestica Borkh), the genome sequence v1 and v2 could not meet this need; therefore, a novel approach was devised to develop a dense genetic linkage map, providing the most reliable marker-loci order for the highest possible number of markers. The approach was based on four strategies: (i) the use of multiple full-sib families, (ii) the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism (SNP) markers, (iii) the construction of a single backcross-type data set including all families, and (iv) a two-step map generation procedure based on the sequential inclusion of markers. The map comprises 15 417 SNP markers, clustered in 3 K HaploBlock markers spanning 1 267 cM, with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM. Moreover, chromosome 5 was oriented according to its homoeologous chromosome 10. This map was useful to improve the apple genome sequence, design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies. Its collinearity with the genome sequences v1 and v3 are reported. To our knowledge, this is the shortest published SNP map in apple, while including the largest number of markers, families and individuals. This result validates our methodology, proving its value for the construction of integrated linkage maps for any outbreeding species.
Collapse
Affiliation(s)
| | | | - Mario Di Guardo
- Plant Breeding, Wageningen University and Research, Wageningen 6700AJ, The Netherlands
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige 38010, Italy
| | | | | | - Sara Longhi
- Plant Breeding, Wageningen University and Research, Wageningen 6700AJ, The Netherlands
| | - Michela Troggio
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige 38010, Italy
| | - Luca Bianco
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige 38010, Italy
| | - Hélène Muranty
- IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, Beaucouzé 49071, France
| | - Giulia Pagliarani
- Department of Agricultural Sciences, University of Bologna, Bologna 40127, Italy
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Bologna 40127, Italy
| | - Thomas Letschka
- Department of Molecular Biology, Laimburg Research Centre for Agriculture and Forestry, Ora 39040, Italy
| | - Lidia Lozano Luis
- Department of Molecular Biology, Laimburg Research Centre for Agriculture and Forestry, Ora 39040, Italy
| | | | - Diego Micheletti
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige 38010, Italy
| | - Marco CAM Bink
- Biometris, Wageningen University and Research, Wageningen 6700AA, The Netherlands
| | - Roeland E Voorrips
- Plant Breeding, Wageningen University and Research, Wageningen 6700AJ, The Netherlands
| | - Ebrahimi Aziz
- Plant Breeding, Wageningen University and Research, Wageningen 6700AJ, The Netherlands
| | - Riccardo Velasco
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige 38010, Italy
| | - François Laurens
- IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, Beaucouzé 49071, France
| | - W Eric van de Weg
- Plant Breeding, Wageningen University and Research, Wageningen 6700AJ, The Netherlands
- ()
| |
Collapse
|