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

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...

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Main Authors: Mohd Shaha, Fakhrur Razi, Liew, Pui Ling, Qamaruz Zaman, Faridah, Nulit, Rosimah, Barin, Jakim, Rolland, Justina, Yong, Hui Yee, Boon, Soo Heong
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Published: PeerJ Inc. 2024
Online Access:http://psasir.upm.edu.my/id/eprint/106253/
https://peerj.com/articles/16570/#
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spelling my.upm.eprints.1062532024-05-12T10:35:16Z http://psasir.upm.edu.my/id/eprint/106253/ Genotyping by sequencing for the construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield related quantitative trait loci Mohd Shaha, Fakhrur Razi Liew, Pui Ling Qamaruz Zaman, Faridah Nulit, Rosimah Barin, Jakim Rolland, Justina Yong, Hui Yee Boon, Soo Heong 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 F1 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 HindIII and TaqI enzymes. Reduced representation libraries (RRL) of 112 F1 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). PeerJ Inc. 2024 Article PeerReviewed Mohd Shaha, Fakhrur Razi and Liew, Pui Ling and Qamaruz Zaman, Faridah and Nulit, Rosimah and Barin, Jakim and Rolland, Justina and Yong, Hui Yee and Boon, Soo Heong (2024) Genotyping by sequencing for the construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield related quantitative trait loci. PeerJ, 12. art. no. e16570. pp. 1-31. ISSN 2167-8359 https://peerj.com/articles/16570/# 10.7717/peerj.16570
institution Universiti Putra Malaysia
building UPM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Putra Malaysia
content_source UPM Institutional Repository
url_provider http://psasir.upm.edu.my/
description 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 F1 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 HindIII and TaqI enzymes. Reduced representation libraries (RRL) of 112 F1 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).
format Article
author Mohd Shaha, Fakhrur Razi
Liew, Pui Ling
Qamaruz Zaman, Faridah
Nulit, Rosimah
Barin, Jakim
Rolland, Justina
Yong, Hui Yee
Boon, Soo Heong
spellingShingle Mohd Shaha, Fakhrur Razi
Liew, Pui Ling
Qamaruz Zaman, Faridah
Nulit, Rosimah
Barin, Jakim
Rolland, Justina
Yong, Hui Yee
Boon, Soo Heong
Genotyping by sequencing for the construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield related quantitative trait loci
author_facet Mohd Shaha, Fakhrur Razi
Liew, Pui Ling
Qamaruz Zaman, Faridah
Nulit, Rosimah
Barin, Jakim
Rolland, Justina
Yong, Hui Yee
Boon, Soo Heong
author_sort Mohd Shaha, Fakhrur Razi
title Genotyping by sequencing for the construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield related quantitative trait loci
title_short Genotyping by sequencing for the construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield related quantitative trait loci
title_full Genotyping by sequencing for the construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield related quantitative trait loci
title_fullStr Genotyping by sequencing for the construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield related quantitative trait loci
title_full_unstemmed Genotyping by sequencing for the construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield related quantitative trait loci
title_sort genotyping by sequencing for the construction of oil palm (elaeis guineensis jacq.) genetic linkage map and mapping of yield related quantitative trait loci
publisher PeerJ Inc.
publishDate 2024
url http://psasir.upm.edu.my/id/eprint/106253/
https://peerj.com/articles/16570/#
_version_ 1800093805257424896
score 13.211869

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