Genotyping by sequencing for the construction of oil palm ( Elaeis guineensis Jacq.) genetic linkage map and mapping of yield related quantitative trait loci.

Autor: Mohd Shaha FR; ACGT Sdn. Bhd. & Laboratories, Bukit Jalil, Kuala Lumpur, Malaysia.; Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia., Liew PL; ACGT Sdn. Bhd. & Laboratories, Bukit Jalil, Kuala Lumpur, Malaysia., Qamaruz Zaman F; Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia., Nulit R; Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia., Barin J; Wisma Pertanian Sabah, Department of Agriculture Sabah, Kota Kinabalu, Sabah, Malaysia., Rolland J; Wisma Pertanian Sabah, Department of Agriculture Sabah, Kota Kinabalu, Sabah, Malaysia., Yong HY; ACGT Sdn. Bhd. & Laboratories, Bukit Jalil, Kuala Lumpur, Malaysia., Boon SH; ACGT Sdn. Bhd. & Laboratories, Bukit Jalil, Kuala Lumpur, Malaysia.
Jazyk: angličtina
Zdroj: PeerJ [PeerJ] 2024 Jan 30; Vol. 12, pp. e16570. Date of Electronic Publication: 2024 Jan 30 (Print Publication: 2024).
DOI: 10.7717/peerj.16570
Abstrakt: Background: Oil palm ( Elaeis guineensis Jacq.) is one of the major oil-producing crops. Improving the quality and increasing the production yield of oil palm have been the primary focuses of both conventional and modern breeding approaches. However, the conventional breeding approach for oil palm is very challenging due to its longevity, which results in a long breeding cycle. Thus, the establishment of marker assisted selection (MAS) for oil palm breeding programs would speed up the breeding pipeline by generating new oil palm varieties that possess high commercial traits. With the decreasing cost of sequencing, Genotyping-by-sequencing (GBS) is currently feasible to many researchers and it provides a platform to accelerate the discovery of single nucleotide polymorphism (SNP) as well as insertion and deletion (InDel) markers for the construction of a genetic linkage map. A genetic linkage map facilitates the identification of significant DNA regions associated with the trait of interest via quantitative trait loci (QTL) analysis.
Methods: A mapping population of 112 F 1 individuals from a cross of Deli dura and Serdang pisifera was used in this study. GBS libraries were constructed using the double digestion method with Hind III and Taq I enzymes. Reduced representation libraries (RRL) of 112 F 1 progeny and their parents were sequenced and the reads were mapped against the E. guineensis reference genome. To construct the oil palm genetic linkage map, informative SNP and InDel markers were used to discover significant DNA regions associated with the traits of interest. The nine traits of interest in this study were fresh fruit bunch (FFB) yield, oil yield (OY), oil to bunch ratio (O/B), oil to dry mesocarp ratio (O/DM) ratio, oil to wet mesocarp ratio (O/WM), mesocarp to fruit ratio (M/F), kernel to fruit ratio (K/F), shell to fruit ratio (S/F), and fruit to bunch ratio (F/B).
Results: A total of 2.5 million SNP and 153,547 InDel markers were identified. However, only a subset of 5,278 markers comprising of 4,838 SNPs and 440 InDels were informative for the construction of a genetic linkage map. Sixteen linkage groups were produced, spanning 2,737.6 cM for the maternal map and 4,571.6 cM for the paternal map, with average marker densities of one marker per 2.9 cM and one per 2.0 cM respectively, were produced. A QTL analysis was performed on nine traits; however, only QTL regions linked to M/F, K/F and S/F were declared to be significant. Of those QTLs were detected: two for M/F, four for K/F and one for S/F. These QTLs explained 18.1-25.6% of the phenotypic variance and were located near putative genes, such as casein kinase II and the zinc finger CCCH domain, which are involved in seed germination and growth. The identified QTL regions for M/F, K/F and S/F from this study could be applied in an oil palm breeding program and used to screen palms with desired traits via marker assisted selection (MAS).
Competing Interests: Fakhrur Razi Mohd Shaha, Pui Ling Liew, Hui Yee Yong and Soo Heong Boon are employed by ACGT Sdn. Bhd. Jakim Barin and Justina Rolland are employees of the Department of Agriculture Sabah.
(© 2024 Mohd Shaha et al.)
Databáze: MEDLINE
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