High density SNP and SSR-based genetic maps of two independent oil palm hybrids

Abstract

BackgroundOil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is invaluable. Previously, genetic linkage maps based on AFLP, RFLP and SSR markers were developed and QTLs for fatty acid composition and yield components identified. High density genetic maps of crosses of different genetic backgrounds are indispensable tools for investigating oil palm genetics. They are also useful for comparative mapping analyses to identify markers closely linked to traits of interest.ResultsA 4.5 K customized oil palm SNP array was developed using the Illumina Infinium platform. The SNPs and 252 SSRs were genotyped on two mapping populations, an intraspecific cross with 87 palms and an interspecific cross with 108 palms. Parental maps with 16 linkage groups (LGs), were constructed for the three fruit forms of E. guineensis (dura, pisifera and tenera). Map resolution was further increased by integrating the dura and pisifera maps into an intraspecific integrated map with 1,331 markers spanning 1,867 cM. We also report the first map of a Colombian E. oleifera, comprising 10 LGs with 65 markers spanning 471 cM. Although not very dense due to the high level of homozygosity in E. oleifera, the LGs were successfully integrated with the LGs of the tenera map. Direct comparison between the parental maps identified 603 transferable markers polymorphic in at least two of the parents. Further analysis revealed a high degree of marker transferability covering 1,075 cM, between the intra- and interspecific integrated maps. The interspecific cross displayed higher segregation distortion than the intraspecific cross. However, inclusion of distorted markers in the genetic maps did not disrupt the marker order and no map expansion was observed.ConclusionsThe high density SNP and SSR-based genetic maps reported in this paper have greatly improved marker density and genome coverage in comparison with the first reference map based on AFLP and SSR markers. Therefore, it is foreseen that they will be more useful for fine mapping of QTLs and whole genome association mapping studies in oil palm.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-309) contains supplementary material, which is available to authorized users.

Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers

“…Both the species have 16 chromosome pairs (2n = 32). Commercial E. guineensis (African oil palm) originated in intertropical Africa (Ting et al, 2014) and was imported into South Asia, where its industrial plantations started approximately 100 years ago. It has become one of the most important crops in Indonesia and Malaysia (Abram et al, 2014;Low et al, 2014).…”

PEMANFAATAN TEKNOLOGI GENOMIKA DAN TRANSFORMASI GENETIK UNTUK MENINGKATKAN PRODUKTIVITAS KELAPA SAWIT / The Use of Genomic and Genetic Transformation Technologies for Oil Palm Productivity Improvement

“…Pengujian ini baru dapat dilakukan setelah tanaman mulai berproduksi dan menghasilkan tandan buah (Singh et al, 2013b;Ting et al, 2014).…”

“…Jutaan SNP yang telah diidentifikasi pada penelitian ini, setelah diverifikasi dapat digunakan untuk mensintesis sistem genotyping kapasitas tinggi (high throughput genotyping system) seperti SNP chip kelapa sawit densitas tinggi untuk percepatan pelebelan gen/QTL unggul (Tasma 2015b;Tasma 2016a). SNP chip ini akan memperkaya SNP chip yang sudah ada saat ini yang terdiri dari 4.451 SNP (Ting et al, 2014). Genotying 199 individu F1 populasi persilangan interspesifik E guineesis x E. Oleifera dapat diselesaikan hanya dalam waktu tiga bulan dan menghasilkan peta genetik dengan kandungan marka molekuler yang padat dibanding peta genetik kelapa sawit sebelumnya berdasarkan marka AFLP dan SSR (Barcelos et al, 2002;Singh et al, 2009;Billotte et al, 2010;Ting et al, 2013).…”

Pedigree-based linkage map in two genetic groups of oil palm

“…The estimated length of this map was 1743 cM. Then, other maps have been reported (Seng et al 2011;Jeennor and Volkaert 2014;Ting et al 2014;Ukoskit et al 2014). In parallel, genetic maps were constructed based on crosses involving E. guineensis and its sister species Elaeis oleifera HBK (Cortès) for QTL mapping.…”