Genomic diversity and genome-wide association analysis related to yield and fatty acid composition of wild American oil palm

Ithnin, Maizura; Vu, Wendy; Shin, Min-Gyoung; Suryawanshi, Vasantika; Sherbina, Katrina; Zolkafli, Siti Hazirah; Serdari, Norhalida Mohamed; Amiruddin, Mohd Din; Abdullah, Norziha; Mustaffa, Suzana; Marjuni, Marhalil; Rajanaidu, N.; Kushairi, A.; Marjoram, Paul; Nuzhdin, Sergey V.; Chang, Peter L.; Singh, Rajinder

doi:10.1016/j.plantsci.2020.110731

Cited by 14 publications

(6 citation statements)

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“…The available gene pool has now been greatly expanded, largely thanks to a series of germplasm collection expeditions to Africa and South America by pioneering breeders such as Rajanaidu et al ( 2014 ). This has now allowed for genome-wide association studies (GWAS) of key traits such as oil yield and fatty acid composition (Ithnin et al 2020 ) in the case of American oil palm and an Elaeis oleifera × Elaeis guineensis hybrid (Osorio-Guarín et al 2019 ). Recent breeding-related reviews include genomics, genomic selection (Nyouma et al 2019 ), transgenics (Costa et al 2012 ), genome editing (Yarra et al 2020 ), and marker-assisted selection (Ting et al 2018 ; Babu et al 2019 ).…”

Section: Breeding and Biotechnology To Improve Oil Palm As A Cropmentioning

confidence: 99%

Oil palm in the 2020s and beyond: challenges and solutions

2021

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Background Oil palm, Elaeis guineensis, is by far the most important global oil crop, supplying about 40% of all traded vegetable oil. Palm oils are key dietary components consumed daily by over three billion people, mostly in Asia, and also have a wide range of important non-food uses including in cleansing and sanitizing products. Main body Oil palm is a perennial crop with a > 25-year life cycle and an exceptionally low land footprint compared to annual oilseed crops. Oil palm crops globally produce an annual 81 million tonnes (Mt) of oil from about 19 million hectares (Mha). In contrast, the second and third largest vegetable oil crops, soybean and rapeseed, yield a combined 84 Mt oil but occupy over 163 Mha of increasingly scarce arable land. The oil palm crop system faces many challenges in the 2020s. These include increasing incidence of new and existing pests/diseases and a general lack of climatic resilience, especially relating to elevated temperatures and increasingly erratic rainfall patterns, plus downstream issues relating to supply chains and consumer sentiment. This review surveys the oil palm sector in the 2020s and beyond, its major challenges and options for future progress. Conclusions Oil palm crop production faces many future challenges, including emerging threats from climate change and pests and diseases. The inevitability of climate change requires more effective international collaboration for its reduction. New breeding and management approaches are providing the promise of improvements, such as much higher yielding varieties, improved oil profiles, enhanced disease resistance, and greater climatic resilience.

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Section: Breeding and Biotechnology To Improve Oil Palm As A Cropmentioning

confidence: 99%

Oil palm in the 2020s and beyond: challenges and solutions

2021

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“… Xia et al (2019) revealed 62 SNP markers that were signifcantly associated with fatty acid content, including palmitic acid content (32 SNPs), oleic acid content (4 SNPs), linoleic acid content (1 SNP), and total oil content (25 SNPs) in oil palm. However, SNP remains costly and consequently limits the broad applications of SNP markers for oil palm improvement using these strategies ( Ithnin et al, 2021 ). In contrast, the polymorphisms obtained using IP markers were easily discernable on simple 1.5–2.0% agarose gels and this would enable rapid screening of a large diverse population.…”

Section: Discussionmentioning

confidence: 99%

Development of Intron Polymorphism Markers and Their Association With Fatty Acid Component Variation in Oil Palm

Yang²,

Sun³

et al. 2022

Front. Plant Sci.

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Oil palm (Elaeis guineensis Jacq.) is a tropical woody oil crop of the palm family and is known as “the oil king of the world,” but its palm oil contains about 50% palmitic acid, which is considered unhealthy for humans. Intron polymorphisms (IP) are highly efficient and easily examined molecular markers located adjacent to exon regions of functional genes, thus may be associated with targeted trait variation. In order to speed up the breeding of oil palm fatty acid composition, the current study identified a total of 310 introns located within 52 candidate genes involved in fatty acid biosynthesis in the oil palm genome. Based on the intron sequences, 205 primer pairs were designed, 64 of which showed polymorphism among 70 oil palm individuals. Phenotypic variation of fatty acid content in the 70 oil palm individuals was also investigated. Association analysis revealed that 13 IP markers were significantly associated with fatty acid content variation, and these IP markers were located on chromosomes 2, 5, 6, 8, 9, and 10 of oil palm. The development of such IP markers may be useful for the genetic improvement of fatty acid composition in oil palm.

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“…At the same time, leaf apex necrosis is developed from base substitution events in transgenic palms ( Yeap et al., 2021 ). In a recent study, the Nuzhdin Lab (USA), in partnership with the MPOB perform sequencing of more then 200 E. oleifera and E. guineensis palm trees from Southeast Asia, Africa, Central and South America (Gene bank accession PRJNA434010) ( Ithnin et al., 2021 ). The above-mentioned reports, there are still some limitations in the prevailing protocols that need further improvement for trait-specific GE and regeneration of mutant plants.…”

Section: Recent Developments In Genome Editing In Palm Treesmentioning

confidence: 99%

Is CRISPR/Cas9 a way forward to fast-track genetic improvement in commercial palms? Prospects and limits

et al. 2022

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Commercially important palms (oil palm, coconut, and date palm) are widely grown perennial trees with tremendous commercial significance due to food, edible oil, and industrial applications. The mounting pressure on the human population further reinforces palms’ importance, as they are essential crops to meet vegetable oil needs around the globe. Various conventional breeding methods are used for the genetic improvement of palms. However, adopting new technologies is crucial to accelerate breeding and satisfy the expanding population’s demands. CRISPR/Cas9 is an efficient genome editing tool that can incorporate desired traits into the existing DNA of the plant without losing common traits. Recent progress in genome editing in oil palm, coconut and date palm are preliminarily introduced to potential readers. Furthermore, detailed information on available CRISPR-based genome editing and genetic transformation methods are summarized for researchers. We shed light on the possibilities of genome editing in palm crops, especially on the modification of fatty acid biosynthesis in oil palm. Moreover, the limitations in genome editing, including inadequate target gene screening due to genome complexities and low efficiency of genetic transformation, are also highlighted. The prospects of CRISPR/Cas9-based gene editing in commercial palms to improve sustainable production are also addressed in this review paper.

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Genomic diversity and genome-wide association analysis related to yield and fatty acid composition of wild American oil palm

Cited by 14 publications

References 50 publications

Oil palm in the 2020s and beyond: challenges and solutions

Oil palm in the 2020s and beyond: challenges and solutions

Development of Intron Polymorphism Markers and Their Association With Fatty Acid Component Variation in Oil Palm

Is CRISPR/Cas9 a way forward to fast-track genetic improvement in commercial palms? Prospects and limits

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