TY - JOUR
T1 - Development and applications of the Oil Palm 78K Infinium® HD SNP Array for linkage analysis and chromosome scanning
AU - Ting, Ngoot Chin
AU - Ordway, Jared M.
AU - van de Weg, Eric
AU - Mohamed Serdari, Norhalida
AU - Low, Eng Ti Leslie
AU - Mustaffa, Suzana
AU - Wischmeyer, Corey
AU - Smulders, Marinus J.M.
AU - Sambanthamurthi, Ravigadevi
AU - Singh, Rajinder
PY - 2023/8/1
Y1 - 2023/8/1
N2 - High-throughput and high-density (HD) genetic marker genotyping systems are critical to optimize the efficiency of oil palm breeding and improvement programmes. This study reports the development of the 78 K Infinium® HD customized SNP array, which was used to genotype a thousand palms of a commercial Deli dura x AVROS pisifera family. A total 64,108 (∼82.0%) polymorphic SNP markers were identified of which, 57, 465 (89.6%) were mapped onto the genetic map that has the largest number of markers published so far in oil palm and holds 14,781 SNPs on 2,363 orphan scaffolds (whose chromosomal locations were unknown), which will improve the existing oil palm reference genome (EG5.1). The SNPs were highly informative based on the parent-to-progeny allelic inheritance analysis. The data demonstrated that 4.3% of the progeny resulted from unintentional self-fertilization of the dura female parent. These unintended ‘selfs’ are highly inbred, which will affect their yield. This study also for the first time, describes the homozygosity in the Deli dura and AVROS pisifera, two important parental lines widely used in commercial seed production. As expected, both the parental palms were highly homozygous, having 138 Mb homozygous regions in common, with 70.3% identical alleles. Such a detailed genetic analysis of the individual palm has been made possible with this customized HD SNP array, which will be a valuable tool for routine application in oil palm improvement programmes. The strategy used to design and apply the array will also be of interest for wider scientific research.
AB - High-throughput and high-density (HD) genetic marker genotyping systems are critical to optimize the efficiency of oil palm breeding and improvement programmes. This study reports the development of the 78 K Infinium® HD customized SNP array, which was used to genotype a thousand palms of a commercial Deli dura x AVROS pisifera family. A total 64,108 (∼82.0%) polymorphic SNP markers were identified of which, 57, 465 (89.6%) were mapped onto the genetic map that has the largest number of markers published so far in oil palm and holds 14,781 SNPs on 2,363 orphan scaffolds (whose chromosomal locations were unknown), which will improve the existing oil palm reference genome (EG5.1). The SNPs were highly informative based on the parent-to-progeny allelic inheritance analysis. The data demonstrated that 4.3% of the progeny resulted from unintentional self-fertilization of the dura female parent. These unintended ‘selfs’ are highly inbred, which will affect their yield. This study also for the first time, describes the homozygosity in the Deli dura and AVROS pisifera, two important parental lines widely used in commercial seed production. As expected, both the parental palms were highly homozygous, having 138 Mb homozygous regions in common, with 70.3% identical alleles. Such a detailed genetic analysis of the individual palm has been made possible with this customized HD SNP array, which will be a valuable tool for routine application in oil palm improvement programmes. The strategy used to design and apply the array will also be of interest for wider scientific research.
KW - Advanced breeding lines
KW - Chromosomal aberration
KW - Elaeis guineensis
KW - Germplasm
KW - Inbreeding
KW - Marker-assisted selection
U2 - 10.1016/j.scienta.2023.112104
DO - 10.1016/j.scienta.2023.112104
M3 - Article
AN - SCOPUS:85157969175
SN - 0304-4238
VL - 318
JO - Scientia Horticulturae
JF - Scientia Horticulturae
M1 - 112104
ER -