Genome-wide identification of markers for selecting higher oil content in oil palm

Bai, Bin; Wang, Le; Lee, May; Zhang, Yingjun; Rahmadsyah,; Alfiko, Yuzer; Ye, Bao Qing; Wan, Zi Yi; Lim, Chin Huat; Suwanto, Antonius; Chua, Nam‐Hai; Yue, Gen Hua

doi:10.1186/s12870-017-1045-z

Cited by 49 publications

(28 citation statements)

References 44 publications

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“…The first SNP discovery in oil palm using ddRAD-seq with Pst I- Msp I was conducted with 3417 informative SNPs 9 . In a later study 32 , 2139 informative SNPs were identified using ddRAD-seq with Pst I- Msp I in an oil palm breeding population, and a high-density SNP genotyping array was developed 40 . In this study, we discovered more than 10,000 informative SNPs using a different approach: single digest RAD-seq with the Pst I 35 , modified for a highly heterozygous breeding oil palm population.…”

Section: Discussionmentioning

confidence: 99%

“…This technique has successfully been applied to discover thousands of markers in plants such as wheat and barley 26 , sorghum 27 , rice 28 , switchgrass 29 , sesame 30 , and in insects and fish 31 . While more than ten genetic linkage maps are available for oil palm, only two linkage maps was based on around 1000 SNPs 9 , 32 .…”

Section: Introductionmentioning

confidence: 99%

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Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm

Bai

Wang

Zhang

et al. 2018

Sci Rep

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Oil palm (Elaeis guineensis Jacq.) is the leading oil-producing crops and the most important edible oil resource worldwide. DNA markers and genetic linkage maps are essential resources for marker-assisted selection to accelerate genetic improvement. We conducted RAD-seq on an Illumina NextSeq500 to discover genome-wide SNPs, and used the SNPs to construct a linkage map for an oil palm (Tenera) population derived from a cross between a Deli Dura and an AVROS Pisifera. The RAD-seq produced 1,076 million single-end reads across the breeding population containing 155 trees. Mining this dataset detected 510,251 loci. After filtering out loci with low accuracy and more than 20% missing data, 11,394 SNPs were retained. Using these SNPs, in combination with 188 anchor SNPs and 123 microsatellites, we constructed a linkage map containing 10,023 markers covering 16 chromosomes. The map length is 2,938.2 cM with an average marker space of 0.29 cM. The large number of SNPs will supply ample choices of DNA markers in analysing the genetic diversity, population structure and evolution of oil palm. This high-density linkage map will contribute to mapping quantitative trait loci (QTL) for important traits, thus accelerating oil palm genetic improvement.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm

Bai

Wang

Zhang

et al. 2018

Sci Rep

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“…SNPs detected by GBS have allowed the genetic dissection of genotypic variation in complex traits in many plant species [34][35][36]. Specifically, in oil palm the GBS technique has been used for identifying candidate genes related to oil bunch [37], bunch weight [20,37], stem height [21] and oil quality traits studies [38] with the enzymes ApeKI and PstI-MspI. Here, we used the enzyme PstI for the library construction, allowing us to identify relatively high number of SNPs with probably novel genetics variants, which according to Chung et al [39] is one of the most important advantages of…”

Section: Association Analysismentioning

confidence: 99%

Genome wide association study (GWAS) for morphological and yield-related traits in oil palm hybrids (Elaeis oleifera x Elaeis guineensis)

Osorio

Garzón

Delgadillo

et al. 2019

Preprint

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Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. The work presented herein provides, to our knowledge, the first association mapping study in an interspecific OxG hybrid population of oil palm which presents tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3,776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrids for 10 agronomic traits. Twelve genomic regions were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on candidate genes that mapped on genomic regions involved in plant architecture and yield; however, these potential candidate genes need to be confirmed for future targeted functional analysis. The associated markers may be valuable resources for the development of marker-assisted selection in oil palm breeding. Keywords: Association mapping, Elaeis guineensis, Elaeis oleifera, genotyping-by-sequencing, plant architecture, yield.

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“…For example, QTL analyses have been conducted for the traits of bunch number, fresh fruit bunch yield, oil yield, oil to bunch content and fatty acid composition 15 – 20 and leaf area 21 . With the advent of next-generation sequencing (NGS) and genotyping by sequencing (GBS), genome-wide association studies (GWAS) have been used to identify the oil yield-related loci 22 – 24 . A GWAS for oil to dry mesocarp content (O/DM) on 2,045 Tenera palms was performed using 200 K SNPs and identified 80 loci which were significantly associated with O/DM 23 .…”

Section: Introductionmentioning

confidence: 99%

Cloning and characterization of EgGDSL, a gene associated with oil content in oil palm

Zhang

Bai

Lee

et al. 2018

Sci Rep

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Oil palm (Elaeis guineensis, Jacq.) is a key tropical oil crop, which provides over one third of the global vegetable oil production, but few genes related to oil yield have been characterized. In this study, a GDSL esterase/lipase gene, which was significantly associated with oil content, was isolated from oil palm and designated as EgGDSL. Its functional characterization was carried out through ectopic expression in Arabidopsis ecotype Col-0. It was shown that expression of EgGDSL in Arabidopsis led to the increased total fatty acid content by 9.5% compared with the wild type. Further analysis of the fatty acid composition revealed that stearic acid (18:0) increased in the seeds of the transgenic lines, but the levels of linoleic acid (18:2) plus 11-eicosenoic acid drastically declined. Quantitative real-time PCR (qPCR) revealed that in oil palm, EgGDSL was highly expressed in mesocarp followed by leaf, and the expression level was very low in the root. The expression level of EgGDSL gene began to increase at two months after flowering (MAF) and reached its peak by four MAF, then declined rapidly, and reached its lowest level during the mature period (6 MAF). The EgGDSL gene was more highly expressed in oil palm trees with high oil content than that with low oil content, demonstrating that the transcription level of EgGDSL correlated with the amount of oil accumulation. The gene may be valuable for engineering fatty acid metabolism in crop improvement programmes and for marker-assisted breeding.

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Genome-wide identification of markers for selecting higher oil content in oil palm

Cited by 49 publications

References 44 publications

Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm

Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm

Genome wide association study (GWAS) for morphological and yield-related traits in oil palm hybrids (Elaeis oleifera x Elaeis guineensis)

Cloning and characterization of EgGDSL, a gene associated with oil content in oil palm

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