Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS)

Abstract

Oil palm has become one of the most important oil crops in the world. Marker-assisted selections have played a pivotal role in oil palm breeding programs. Here, we report the use of genotyping-by-sequencing (GBS) approach for a large-scale SNP discovery and genotyping of a mapping population. Reduced representation libraries of 108 F2 progeny were sequenced and a total of 524 million reads were obtained. We detected 21,471 single nucleotide substitutions, most of which (62.6%) represented transition events. Of 3417 fully informative SNP markers, we were able to place 1085 on a linkage map, which spanned 1429.6 cM and had an average of one marker every 1.26 cM. Three QTL affecting trunk height were detected on LG 10, 14 and 15, whereas a single QTL associated with fruit bunch weight was identified on LG 3. The use of GBS approach proved to be rapid, cost-effective and highly reproducible in this species.

Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach

“…This higher transition rate was also observed in oil palm. In oil palm and Miscanthus sinensis, the most prevalent substitution types were A/G and C/T (Ma et al 2012;Pootakham et al 2015). These substitutions were also the most prevalent substitution types identified in this study.…”

“…The average frequency of sunflower SNPs identified in this study was 72 kb/SNP (1 SNP every 72 kb); this is higher than soybean (100 kb/SNP) (Sonah et al 2013) and much lower than the frequency identified in oil palm (1 SNP in 0.665 kb) (Pootakham et al 2015). Again, the higher frequency of SNPs in oil palm could reflect the higher number of reads and higher coverage of the oil palm alignment (88 %).…”

“…Although this set represented only 1.7 % of the unfiltered SNPs, exclusion of most of the SNPs due to missing data or segregation distortion was also observed in other GBS linkage mapping studies performed in apple (0.9 % of total identified SNPs retained) and oil palm (5 % retained) (Pootakham et al 2015;Gardner et al, 2014). The total size of the sunflower linkage map (2472 cM) was larger than previous SNP marker maps reported by Talukder et al (2014) (1444 cM) and Bowers et al (2012) (1080 cM).…”

“…LG 13 number of reads (524,508,111) with 88 % of the total reads aligned to unique locations in the oil palm genome (Pootakham et al 2015). This higher alignment percentage stresses the importance of the genome because oil palm has a complete genome sequence (Singh et al 2013) while the current assembly of the sunflower genome represents only 85 % of the complete genome.…”

“…These species include barley (Elshire et al 2011), Miscanthus sinensis (Ma et al 2012), Rubus idaeus (Ward et al 2013) and maize (Romay et al 2013). Also GBS was applied in an F 2 population of oil palm to identify 21,471 SNPs and to construct a linkage map containing 1085 SNPs (Pootakham et al 2015).…”