Anchoring a genetic map of an interspecific backcross two family to the genome builds of Elaeis

• Published in: Journal of genetics Vol. 100; no. 1
• Main Authors: KAMARUDDIN, KATIALISA, ITHNIN, MAIZURA, TING, NGOOT-CHIN, YAAKUB, ZULKIFLI, SANUSI, NIK SHAZANA NIK MOHD, SRITHARAN, KANDHA, SINGH, RAJINDER
• Format: Journal Article
• Language: English
• Published: New Delhi Springer India 2021; Springer; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Biomedical and Life Sciences; Chromosome 2; Chromosome 3; Elaeis guineensis; Elaeis oleifera; Evolutionary Biology; Fatty acid composition; Gene mapping; Genetic aspects; Genomes; Genomics; Hybrids; Interspecific; Iodine; Life Sciences; Linoleic acid; Microbial Genetics and Genomics; Palmitic acid; Plant Genetics and Genomics; Population; Population genetics; Quantitative genetics; Quantitative trait loci; Research Article; Saturated fatty acids; Single-nucleotide polymorphism; Unsaturated fatty acids; physical map; single-nucleotide polymorphism; .; simple-sequence repeat
• ISSN: 0022-1333; 0973-7731
• DOI: 10.1007/s12041-020-01240-8

The present study evaluated an interspecific backcross two (BC 2 ) population of oil palm, which was segregating for fatty acid composition (FAC). The purpose of this study was to construct a high-density genetic map for the population, which could be used to anchor the Elaeis guineensis (EG5) and E. oleifera (O7) genome builds and determine the physical positions of the quantitative trait loci (QTLs) associated with FAC. A high-density SNP-based and SSR-based linkage map was successfully constructed for an E. guineensis  ×  E. oleifera BC 2 population. The genetic map had 16 linkage groups spanning 1618.4 cM with 1252 markers (1152 SNPs and 100 SSRs). The physical location of the markers were determined through sequence similarity search against EG5 and O7. The majority of markers (81.2%) showed map order consistent with their corresponding position on EG5. In total, 1218 markers were also anchored to 683 scaffolds in O7. This study for the first time compared the genetic map of the BC 2 population with that of a published E. oleifera  ×  E. guineensis (O×G) interspecific F 1 hybrid, which revealed 433 common markers (34.6%). More importantly marker order was generally consistent in both maps. The published EG5 facilitated orientating the mapped markers in the present BC 2 map as well as in the O7 scaffolds. Major QTLs associated with iodine value (IV) and palmitic acid (C16:0) content, localized on chromosome 3 and linoleic acid (C18:2) content localized on chromosome 2 of EG5 were also for the first time positioned on the O7 build, revealing the corresponding position in the E. oleifera genome likely influencing FAC in hybrids and backcrosses.