Genome-wide association study (GWAS) for stem height increment in oil palm (Elaeis guineensis) germplasm using SNP markers
- 91 Downloads
Oil palm germplasms belonging to four African countries were used in GWAS for stem height increment. Till now, there has been no report available on GWAS study of African oil palm germplasm using single-nucleotide polymorphisms (SNPs) by genotyping by sequencing (GBS) method for height increment. GBS generated a total of 325 million reads covering 50.78 Gb of sequence data, with an average of 3.4 million reads per sample. For the final dataset, we were able to retain 4031 SNPs across the 96 genotypes. The range of height increment varied from 11.43 to 58.21 cm at an average of 29.19 cm. Association mapping resulted in identification of five significant quantitative trait loci (QTLs) on chromosome 6, 7, and 9. Interestingly, three QTLs located on chromosome 7 itself, while one each on chromosome 6 and 9 at a P value of < 0.00001. Out of the five QTLs, qtlH7.1 on chromosome 7 was found to be highly significant which explained a phenotypic variance of 15% at a P of 2 × 10−5. The blast results of qtlH7.1 showed that it was found to be more similar to oil palm B3 domain containing protein (LOC 105043719) transcript variant X3, mRNA. The B3 domain containing proteins consisted of families like auxin response factors (ARFs) and abscisic acid insensitive 3 (ABI3). These results showed that qtlH7.1 might be playing an important role in stem height increment. The QTLs identified in the present study could be used in selection of oil palm germplasm for low height increment.
KeywordsOil palm Height increment Genotyping by sequencing Genome-wide association mapping
The authors also thankful to Dr. Arun Kumar for statistical analysis for stem height increment.
BK, RKM, and MVB performed the experiments; BK analyzed the data; BK, RKM, and GR wrote and reviewed the manuscript.
DST-SERB (YSS/2015/001837) and Indian Council of Agricultural Research provided financial support.
Compliance with ethical standards
Conflict of interest
The authors declare that there is no conflict of interest.
- Alonso R, Oñate-Sánchez L, Weltmeier F, Ehlert A, Díaz I, Dietrich K, Vicente-Carbajosa J, Droge-Laser W (2009) A pivotal role of the basic leucine zipper transcription factor bZIP53 in the regulation of Arabidopsis seed maturation gene expression based on heterodimerization and protein complex formation. Plant Cell 21:1747–1761CrossRefGoogle Scholar
- Babu BK, Mathur RK, Kumar PN, Ramajayam D, Ravichandran G, Venu MVB (2017) Development, identification and validation of CAPS marker for SHELL trait which governs dura, pisifera and tenera fruit forms in oil palm (Elaeis guineensis Jacq.). PLoS One 12(2):e0171933. https://doi.org/10.1371/journal.pone.0171933 CrossRefPubMedPubMedCentralGoogle Scholar
- Begum H, Spindel JE, Lalusin A, Borromeo T, Gregorio G, Hernandez J (2015) Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical Rice (Oryza sativa). PLoS One 10(3):e0119873. https://doi.org/10.1371/journal.pone.0119873 CrossRefPubMedPubMedCentralGoogle Scholar
- Ganal MW, Durstewitz G, Polley A, Bérard A, Buckler ES, Charcosset A (2011) A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One 6(12):e28334. https://doi.org/10.1371/journal.pone.0028334 CrossRefPubMedPubMedCentralGoogle Scholar
- Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang QF, Li J, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42(11):961–967CrossRefGoogle Scholar
- Jia G, Huang X, Zhi H, Zhao Y, Zhao Q, Li W, Chai Y, Yang L, Liu K, Lu H, Zhu C, Lu Y, Zhou C, Fan D, Weng Q, Guo Y, Huang T, Zhang L, Lu T, Feng Q, Hao H, Liu H, Lu P, Zhang N, Li Y, Guo E, Wang S, Wang S, Liu J, Zhang W, Chen G, Zhang B, Li W, Wang Y, Li H, Zhao B, Li J, Diao X, Han B (2013) A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet 45:957–961CrossRefGoogle Scholar
- JMP (2009). Version 8.02. SAS Institute, Cary, NCGoogle Scholar
- Morcillo F, Gagneur C, Adam H, Richaud F, Singh R, Cheah SC, Rival A, Duval Y, Tregear JW (2006) Somaclonal variation in micropropagated oil palm. Characterization of two novel genes with enhanced expression in epigenetically abnormal cell lines and in response to auxin. Tree Physiol 26:585–594CrossRefGoogle Scholar
- Murphy DJ (2014) The future of oil palm as a major global crop: opportunities and challenges. J Oil Palm Res 26:1–24Google Scholar
- Pritchard JK, Wen W (2003) Documentation for the structure software, version 2. Department of Human Genetics, University of Chicago, Chicago. http://pritch.bsd.uchicago.edu/software. Accessed 3 March 2014
- Turner PD, Gillbanks RA (1974) Oil palm cultivation and management, 1st edn. The incorporated society of planter, Kuala LampurGoogle Scholar