High-density single nucleotide polymorphism （SNP） genotyping arrays are powerful tools that can measure the level of genetic polymorphism within a population. To develop a whole-genome SNP array for oil palms, SNP d...High-density single nucleotide polymorphism （SNP） genotyping arrays are powerful tools that can measure the level of genetic polymorphism within a population. To develop a whole-genome SNP array for oil palms, SNP discovery was performed using deep resequencing of eight libraries derived from 132 Elaeis guineen- sis and Elaeis oleifera palms belonging to 59 origins, resulting in the discovery of 〉3 million putative SNPs. After SNP filtering, the Illumina OP200K custom array was built with 170 860 successful probes. Phenetic clustering analysis revealed that the array could distinguish between palms of different origins in a way consistent with pedigree records. Genome-wide linkage disequilibrium declined more slowly for the commercial populations （ranging from 120 kb at r2 = 0.43 to 146 kb at r2 = 0.50） when compared with the semi-wild populations （19.5 kb at r2 = 0.22）. Genetic fixation mapping comparing the semi-wild and commercial population identified 321 selective sweeps. A genome-wide association study （GWAS） detected a significant peak on chromosome 2 associated with the polygenic component of the shell thick- ness trait （based on the trait shell-to-fruit; S/F %） in tenera palms. Testing of a genomic selection model on the same trait resulted in good prediction accuracy （r = 0.65） with 42% of the S/F % variation explained. The first high-density SNP genotyping array for oil palm has been developed and shown to be robust for use in genetic studies and with potential for developing early trait prediction to shorten the oil palm breeding cycle.展开更多
Over the past 70 years,the world has witnessed extraordinary growth in crop productivity,enabled by a suite of technological advances,including higher yielding crop varieties,improved farm management,synthetic agroche...Over the past 70 years,the world has witnessed extraordinary growth in crop productivity,enabled by a suite of technological advances,including higher yielding crop varieties,improved farm management,synthetic agrochemicals,and agricultural mechanization.While this"Green Revolution"intensified crop production,and is credited with reducing famine and malnutrition,its benefits were accompanied by several undesirable collateral effects(Pingali,2012).These include a narrowing of agricultural biodiversity,stemming from increased monoculture and greater reliance on a smaller number of crops and crop varieties for the majority of our calories.This reduction in diversity has created vulnerabilities to pest and disease epidemics,climate variation,and ultimately to human health(Harlan,1972).展开更多
文摘High-density single nucleotide polymorphism （SNP） genotyping arrays are powerful tools that can measure the level of genetic polymorphism within a population. To develop a whole-genome SNP array for oil palms, SNP discovery was performed using deep resequencing of eight libraries derived from 132 Elaeis guineen- sis and Elaeis oleifera palms belonging to 59 origins, resulting in the discovery of 〉3 million putative SNPs. After SNP filtering, the Illumina OP200K custom array was built with 170 860 successful probes. Phenetic clustering analysis revealed that the array could distinguish between palms of different origins in a way consistent with pedigree records. Genome-wide linkage disequilibrium declined more slowly for the commercial populations （ranging from 120 kb at r2 = 0.43 to 146 kb at r2 = 0.50） when compared with the semi-wild populations （19.5 kb at r2 = 0.22）. Genetic fixation mapping comparing the semi-wild and commercial population identified 321 selective sweeps. A genome-wide association study （GWAS） detected a significant peak on chromosome 2 associated with the polygenic component of the shell thick- ness trait （based on the trait shell-to-fruit; S/F %） in tenera palms. Testing of a genomic selection model on the same trait resulted in good prediction accuracy （r = 0.65） with 42% of the S/F % variation explained. The first high-density SNP genotyping array for oil palm has been developed and shown to be robust for use in genetic studies and with potential for developing early trait prediction to shorten the oil palm breeding cycle.
文摘Over the past 70 years,the world has witnessed extraordinary growth in crop productivity,enabled by a suite of technological advances,including higher yielding crop varieties,improved farm management,synthetic agrochemicals,and agricultural mechanization.While this"Green Revolution"intensified crop production,and is credited with reducing famine and malnutrition,its benefits were accompanied by several undesirable collateral effects(Pingali,2012).These include a narrowing of agricultural biodiversity,stemming from increased monoculture and greater reliance on a smaller number of crops and crop varieties for the majority of our calories.This reduction in diversity has created vulnerabilities to pest and disease epidemics,climate variation,and ultimately to human health(Harlan,1972).
