High density SNP and DArT-based genetic linkage maps of two closely related oil palm populations

Oil palm (Elaeis guineensis Jacq.) is an outbreeding perennial tree crop with long breeding cycles, typically 12 years. Molecular marker technologies can greatly improve the breeding efficiency of oil palm. This study reports the first use of the DArTseq platform to genotype two closely related self-pollinated oil palm populations, namely AA0768 and AA0769 with 48 and 58 progeny respectively. Genetic maps were constructed using the DArT and SNP markers generated in combination with anchor SSR markers. Both maps consisted of 16 major independent linkage groups (2n = 2× = 32) with 1399 and 1466 mapped markers for the AA0768 and AA0769 populations, respectively, including the morphological trait “shell-thickness” (Sh). The map lengths were 1873.7 and 1720.6 cM with an average marker density of 1.34 and 1.17 cM, respectively. The integrated map was 1803.1 cM long with 2066 mapped markers and average marker density of 0.87 cM. A total of 82% of the DArTseq marker sequence tags identified a single site in the published genome sequence, suggesting preferential targeting of gene-rich regions by DArTseq markers. Map integration of higher density focused around the Sh region identified closely linked markers to the Sh, with D.15322 marker 0.24 cM away from the morphological trait and 5071 bp from the transcriptional start of the published SHELL gene. Identification of the Sh marker demonstrates the robustness of using the DArTseq platform to generate high density genetic maps of oil palm with good genome coverage. Both genetic maps and integrated maps will be useful for quantitative trait loci analysis of important yield traits as well as potentially assisting the anchoring of genetic maps to genomic sequences

Genetic diversity and population structure of the upriver orange mangrove Bruguiera sexangula along the coastlines of Thailand

Upriver orange mangrove Bruguiera sexangula is a member of the Rhizophoraceae family and is usually distributed in the intertidal zones of the tropical and subtropical coastal areas. The analyses of genetic diversity and population structure of B. sexangula are essential for their conservation and management. In the present study, the genetic diversity and structure of 101 B. sexangula individuals from mangrove forests in Thailand were evaluated using single nucleotide polymorphisms (SNPs) through restriction site-associated DNA sequencing (RAD-seq). A total of 3482 high-quality SNPs were obtained after filtration for genetic study. All 3 genetic structure analyses (Bayesian analysis, principal components analysis, and maximum likelihood tree) revealed that these individuals can be clustered into 2 groups corresponding to geographical regions, namely the Andaman Sea and Gulf of Thailand. The level of genetic differentiation between the clusters was moderate (FST = 0.122, p < 0.001), and the analysis of molecular variance (AMOVA) indicated that the individual differences within groups were greater than the differences between the 2 groups. A moderate level of genetic diversity (Shannon's information index, I = 0.458; observed heterozygosity, Ho = 0.416; expected heterozygosity, He = 0.295) of B. sexangula was observed. These results give us a better understanding of the genetic variations and will provide a framework for the conservation of B. sexangula

2002 Research Honors Program Abstracts

Faculty in the College of Agriculture and Life Sciences at Cornell University mentor and guide undergraduate students who have chosen to pursue a research project and graduate with honors. These abstracts reflect the depth of their scholarship and intellectual ability. The research projects encompass work in animal science, biological science, entomology, natural resources, physical science, plant science, and social science