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Fulltext 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 FR, Liew PL, Qamaruz Zaman F, Nulit R, Barin J, Rolland J, et al.

PeerJ, 2024;12:e16570.

PMID: 38313025 DOI: 10.7717/peerj.16570

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).

Matched MeSH terms: Chromosome Mapping

Molecular progress on the mapping and cloning of functional genes for blast disease in rice (Oryza sativa L.): current status and future considerations

Ashkani S, Rafii MY, Shabanimofrad M, Ghasemzadeh A, Ravanfar SA, Latif MA

Crit Rev Biotechnol, 2016;36(2):353-67.

PMID: 25394538 DOI: 10.3109/07388551.2014.961403

Rice blast disease, which is caused by the fungal pathogen Magnaporthe oryzae, is a recurring problem in all rice-growing regions of the world. The use of resistance (R) genes in rice improvement breeding programmes has been considered to be one of the best options for crop protection and blast management. Alternatively, quantitative resistance conferred by quantitative trait loci (QTLs) is also a valuable resource for the improvement of rice disease resistance. In the past, intensive efforts have been made to identify major R-genes as well as QTLs for blast disease using molecular techniques. A review of bibliographic references shows over 100 blast resistance genes and a larger number of QTLs (∼500) that were mapped to the rice genome. Of the blast resistance genes, identified in different genotypes of rice, ∼22 have been cloned and characterized at the molecular level. In this review, we have summarized the reported rice blast resistance genes and QTLs for utilization in future molecular breeding programmes to introgress high-degree resistance or to pyramid R-genes in commercial cultivars that are susceptible to M. oryzae. The goal of this review is to provide an overview of the significant studies in order to update our understanding of the molecular progress on rice and M. oryzae. This information will assist rice breeders to improve the resistance to rice blast using marker-assisted selection which continues to be a priority for rice-breeding programmes.

Matched MeSH terms: Chromosome Mapping*

High density SNP and DArT-based genetic linkage maps of two closely related oil palm populations

Gan ST, Wong WC, Wong CK, Soh AC, Kilian A, Low EL, et al.

J Appl Genet, 2018 Feb;59(1):23-34.

PMID: 29214520 DOI: 10.1007/s13353-017-0420-7

Oil palm (Elaeis guineensis Jacq.) is an outbreeding perennial tree crop with long breeding cycles, typically 12 years. Molecular marker technologies can greatly improve the breeding efficiency of oil palm. This study reports the first use of the DArTseq platform to genotype two closely related self-pollinated oil palm populations, namely AA0768 and AA0769 with 48 and 58 progeny respectively. Genetic maps were constructed using the DArT and SNP markers generated in combination with anchor SSR markers. Both maps consisted of 16 major independent linkage groups (2n = 2× = 32) with 1399 and 1466 mapped markers for the AA0768 and AA0769 populations, respectively, including the morphological trait "shell-thickness" (Sh). The map lengths were 1873.7 and 1720.6 cM with an average marker density of 1.34 and 1.17 cM, respectively. The integrated map was 1803.1 cM long with 2066 mapped markers and average marker density of 0.87 cM. A total of 82% of the DArTseq marker sequence tags identified a single site in the published genome sequence, suggesting preferential targeting of gene-rich regions by DArTseq markers. Map integration of higher density focused around the Sh region identified closely linked markers to the Sh, with D.15322 marker 0.24 cM away from the morphological trait and 5071 bp from the transcriptional start of the published SHELL gene. Identification of the Sh marker demonstrates the robustness of using the DArTseq platform to generate high density genetic maps of oil palm with good genome coverage. Both genetic maps and integrated maps will be useful for quantitative trait loci analysis of important yield traits as well as potentially assisting the anchoring of genetic maps to genomic sequences.

Matched MeSH terms: Chromosome Mapping*

Fulltext Draft Genome Sequence of Paenibacillus sp. Strain MSt1 with Broad Antimicrobial Activity, Isolated from Malaysian Tropical Peat Swamp Soil

Aw YK, Ong KS, Yule CM, Gan HM, Lee SM

Genome Announc, 2014;2(5).

PMID: 25301658 DOI: 10.1128/genomeA.01024-14

We report the draft genome sequence of Paenibacillus sp. strain MSt1, which has broad-range antimicrobial activity, isolated from tropical peat swamp soil. Genes involved in antimicrobial biosynthesis are found to be present in this genome.

Matched MeSH terms: Chromosome Mapping

Fulltext Draft Genome Sequence of Erwinia mallotivora BT-MARDI, Causative Agent of Papaya Dieback Disease

Redzuan RA, Abu Bakar N, Rozano L, Badrun R, Mat Amin N, Mohd Raih MF

Genome Announc, 2014;2(3).

PMID: 24812220 DOI: 10.1128/genomeA.00375-14

Erwinia mallotivora was isolated from papaya trees infected with dieback disease, which were planted at the Malaysian Agricultural Research and Development Institute (MARDI), Malaysia. Here, we report a draft genome sequence of E. mallotivora BT-MARDI, which offers an important source of information for understanding pathogen and host interaction during papaya dieback development.

Matched MeSH terms: Chromosome Mapping

Fulltext Draft Genome Sequences of Two Cellulolytic Paenibacillus sp. Strains, MAEPY1 and MAEPY2, from Malaysian Landfill Leachate

Chua P, Yoo HS, Gan HM, Lee SM

Genome Announc, 2014;2(1).

PMID: 24526641 DOI: 10.1128/genomeA.00065-14

We report the draft genome sequences of two Paenibacillus species with cellulose-degrading abilities isolated from landfill leachate. An array of genes putatively involved in cellulose degradation have been identified in both genome sequences, which can benefit various biotechnological industries.

Matched MeSH terms: Chromosome Mapping

Fulltext Draft Genome Sequence of Klebsiella pneumoniae Isolate PR04

Zulkifli MH, Teh LK, Lee LS, Zakaria ZA, Salleh MZ

Genome Announc, 2013;1(4).

PMID: 23950113 DOI: 10.1128/genomeA.00418-13

Klebsiella pneumoniae PR04 was isolated from a patient hospitalized in Malaysia. The draft genome sequence of K. pneumoniae PR04 shows differences compared to the reference sequences of K. pneumoniae strains MGH 78578 and NTUH-K2044 in terms of their genomic structures.

Matched MeSH terms: Chromosome Mapping

Fulltext Draft Genome Sequence of a Clinical Isolate of Mycobacterium tuberculosis Strain PR05

Ismail A, Teh LK, Ngeow YF, Norazmi MN, Zainul ZF, Tang TH, et al.

Genome Announc, 2013;1(3).

PMID: 23788553 DOI: 10.1128/genomeA.00397-13

We report the annotated genome sequence of a clinical isolate, Mycobacterium tuberculosis strain PR05, which was isolated from the human cerebrospinal fluid of a patient diagnosed with tuberculosis.

Matched MeSH terms: Chromosome Mapping

Fulltext Draft Genome Perspective of Staphylococcus saprophyticus Strain SU8, an N-Acyl Homoserine Lactone-Degrading Bacterium

Chan KG, Sulaiman J, Yong DA, Tee KK, Yin WF, Priya K

Genome Announc, 2015;3(5).

PMID: 26404582 DOI: 10.1128/genomeA.01097-15

Staphylococcus saprophyticus strain SU8 was isolated from a pristine water source in Malaysia and it exhibited degradation of N-hexanoylhomoserine lactone. Here we report the draft genome sequence of S. saprophyticus strain SU8 to further understand its quorum quenching abilities.

Matched MeSH terms: Chromosome Mapping

Fulltext First High-Quality Draft Genome Sequence of Pasteurella multocida Sequence Type 128 Isolated from Infected Bone

Kavousi N, Eng WW, Lee YP, Tan LH, Thuraisingham R, Yule CM, et al.

Genome Announc, 2016;4(2).

PMID: 26941132 DOI: 10.1128/genomeA.00023-16

We report here the first high-quality draft genome sequence of Pasteurella multocida sequence type 128, which was isolated from the infected finger bone of an adult female who was bitten by a domestic dog. The draft genome will be a valuable addition to the scarce genomic resources available for P. multocida.

Matched MeSH terms: Chromosome Mapping

Fulltext Annotated Sequence of Mycobacterium tuberculosis MTBR3/09 Isolated from a Sputum Sample in Malaysia

Issa R, Seradja VH, Abdullah MK, Abdul H

Genome Announc, 2016;4(3).

PMID: 27340055 DOI: 10.1128/genomeA.00517-16

This is a report of the annotated genome sequence of Mycobacterium tuberculosis MTBR3/09. The organism was isolated from a sputum sample in Malaysia.

Matched MeSH terms: Chromosome Mapping

Fulltext Draft Genome Sequence of the Prazosin-Degrading Bacillus sp. Strain PR5, Isolated from a River Receiving Hospital and Urban Wastewater in Malaysia

Ahmad Sabri NS, Mohd Mohsi NF, Apandi A, Yusof N, Megat Mohd Noor MJ, Md Akhir FN, et al.

Microbiol Resour Announc, 2021 Mar 18;10(11).

PMID: 33737348 DOI: 10.1128/MRA.00025-21

We report the complete genome sequence of Bacillus sp. strain PR5, isolated from a river receiving hospital and urban wastewater in Malaysia, which demonstrated a high capability for degrading prazosin. This genome sequence of 4,525,264 bp exhibited 41.5% GC content, 4,402 coding sequences, and 32 RNAs.

Matched MeSH terms: Chromosome Mapping

Fulltext Draft Genome Sequence of Plant Growth-Promoting Rhizobacterium Burkholderia sp. Strain USMB20, Isolated from Nodules of Mucuna bracteata

Aziz NA, Shaffie S, Rahman AYA, Hokchai Y, Najimudin N, Ghazali AHA

Microbiol Resour Announc, 2021 Mar 18;10(11).

PMID: 33737365 DOI: 10.1128/MRA.01051-20

Burkholderia sp. strain USMB20 is a plant growth-promoting rhizobacterium that was isolated from nodules of the leguminous cover crop Mucuna bracteata. The draft genome sequence of Burkholderia sp. strain USMB20 has an assembly size of 7.7 Mbp in 26 contigs with a GC content of 66.88%.

Matched MeSH terms: Chromosome Mapping

Genetic architecture of Al3+ toxicity tolerance in rice F2:3 populations determined through QTL mapping

Jahan N, Javed MA, Khan A, Manan FA, Tabassum B

Ecotoxicology, 2021 Jul;30(5):794-805.

PMID: 33871748 DOI: 10.1007/s10646-021-02413-6

Aluminum (Al3+) toxicity is one of the factors limiting crop production in acidic soils. Identifying quantitative trait loci (QTLs)/genes for tolerance to Al3+ toxicity at seed germination can aid the development of new tolerant cultivars. The segregating population derived from Pak Basmati (Indica) × Pokkali (Indica) was used for mapping QTLs linked with tolerance to Al3+ toxicity ranging from 0 to 20 mM at pH 4 ± 0.2 at germination. The favorable alleles for all new QTLs were analyzed based on germination traits, i.e., final germination percentage (FG%), germination energy (GE), germination speed (GS), germination index (GI), mean germination time (MGT), germination value (GV), germination velocity (GVe), peak value of germination (GPV), and germination capacity (GC), and growth traits, such as root length (RL), shoot length (SL), total dry biomass (TDB) and germination vigor index (GVI). The phenotypic evolution showed transgressive variations. For genome-wide mapping, 90 polymorphic SSRs with 4 gene-specific markers and Win QTL Cart were used for QTL analysis. In all, 35 QTLs for germination and 11 QTLs for seedling growth were detected in distinct chromosomal regions by composite interval mapping (CIM), and multiple interval mapping (MIM) confirmed the pleiotropy at region RM128 on chromosome 1. Based on our genetic mapping studies, the genes/QTLs underlying tolerance to Al3+ toxicity could differ for both the germination and seedling stages in segregated populations. The QTLs identified in this study could be a source of new alleles for improving tolerance to Al3+ toxicity in rice.

Matched MeSH terms: Chromosome Mapping

Fulltext Draft Genome Sequence of Burkholderia sp. Strain CCA53, Isolated from Leaf Soil

Akita H, Kimura Z, Yusoff MZ, Nakashima N, Hoshino T

Genome Announc, 2016;4(4).

PMID: 27389268 DOI: 10.1128/genomeA.00630-16

Burkholderia sp. strain CCA53 was isolated from leaf soil collected in Higashi-Hiroshima City in Hiroshima Prefecture, Japan. Here, we present a draft genome sequence of this strain, which consists of a total of 4 contigs containing 6,647,893 bp, with a G+C content of 67.0% and comprising 9,329 predicted coding sequences.

Matched MeSH terms: Chromosome Mapping

Fulltext Whole-Genome Shotgun Sequencing and Annotation of Mycobacterium tuberculosis MTB221/11 Isolated from a Cerebrospinal Fluid Sample in Malaysia

Issa R, Seradja VH, Abdullah MK

Genome Announc, 2016;4(3).

PMID: 27365342 DOI: 10.1128/genomeA.00376-16

Here, we report of the annotated genome sequence of Mycobacterium tuberculosis MTB221/11. The organism was isolated from the cerebrospinal fluid of a patient in Malaysia.

Matched MeSH terms: Chromosome Mapping

Fulltext Draft Genome Sequence of Rhizoctonia solani Anastomosis Group 1 Subgroup 1A Strain 1802/KB Isolated from Rice

Nadarajah K, Mat Razali N, Cheah BH, Sahruna NS, Ismail I, Tathode M, et al.

Genome Announc, 2017 Oct 26;5(43).

PMID: 29074665 DOI: 10.1128/genomeA.01188-17

Sheath blight, caused by Rhizoctonia solani anastomosis group 1 subgroup 1A (AG1-1A), is one of the most devastating rice diseases worldwide. Here, we report the draft genome sequence of R. solani AG1-1A strain 1802/KB isolated from a popular Malaysian rice variety. To the best of our knowledge, this is the second reported representative genome from AG1-1A.

Matched MeSH terms: Chromosome Mapping

Fulltext Complete Genome Sequence of Streptomyces sp. TN58, a Producer of Acyl Alpha-l-Rhamnopyranosides

Najah S, Chong TM, Gerbaud C, Chan KG, Mellouli L, Pernodet JL

Genome Announc, 2017 Aug 24;5(34).

PMID: 28839022 DOI: 10.1128/genomeA.00828-17

Streptomyces sp. TN58, isolated from a Tunisian soil sample, produces several natural products, including acyl alpha-l-rhamnopyranosides. It possesses a 7.6-Mb linear chromosome. This is, to our knowledge, the first genome sequence of a microorganism known to produce acyl alpha-l-rhamnopyranosides, and it will be helpful to study the biosynthesis of these specialized metabolites.

Matched MeSH terms: Chromosome Mapping

Fulltext Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater

Robledo-Ruiz DA, Gan HM, Kaur P, Dudchenko O, Weisz D, Khan R, et al.

Gigascience, 2022 Mar 29;11.

PMID: 35348671 DOI: 10.1093/gigascience/giac025

BACKGROUND: The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage map are required.

RESULTS: We used a combination of Illumina, Oxford Nanopore, and Hi-C sequencing technologies to assemble a chromosome-length genome of the helmeted honeyeater, comprising 906 scaffolds, with length of 1.1 Gb and scaffold N50 of 63.8 Mb. Annotation comprised 57,181 gene models. Using a pedigree of 257 birds and 53,111 single-nucleotide polymorphisms, we obtained high-density linkage and recombination maps for 25 autosomes and Z chromosome. The total sex-averaged linkage map was 1,347 cM long, with the male map being 6.7% longer than the female map. Recombination maps revealed sexually dimorphic recombination rates (overall higher in males), with average recombination rate of 1.8 cM/Mb. Comparative analyses revealed high synteny of the helmeted honeyeater genome with that of 3 passerine species (e.g., 32 Hi-C scaffolds mapped to 30 zebra finch autosomes and Z chromosome). The genome assembly and linkage map suggest that the helmeted honeyeater exhibits a fission of chromosome 1A into 2 chromosomes relative to zebra finch. PSMC analysis showed a ∼15-fold decline in effective population size to ∼60,000 from mid- to late Pleistocene.

CONCLUSIONS: The annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater.

Matched MeSH terms: Chromosome Mapping

Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae

Low EL, Chan KL, Zaki NM, Taranenko E, Ordway JM, Wischmeyer C, et al.

G3 (Bethesda), 2024 Sep 04;14(9).

PMID: 38918881 DOI: 10.1093/g3journal/jkae135

Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale E. oleifera genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping, and genetic mapping. High interspecific genome conservation is observed between the two species. The study provides the most extensive gene annotation to date, including 46,697 E. guineensis and 38,658 E. oleifera gene predictions. Analyses of repetitive element families further resolve the DNA repeat architecture of both genomes. Comparative genomic analyses identified experimentally validated small structural variants between the oil palm species and resolved the mechanism of chromosomal fusions responsible for the evolutionary descending dysploidy from 18 to 16 chromosomes.

Matched MeSH terms: Chromosome Mapping

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