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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Publications at this Location » Publication #285888
Title: Design of an Illumina Infinium 6k SNPchip for genotyping two large avocado mapping populations

Author
item Kuhn, David
item LININGSTONE III, DONALD - Mars, Inc
item MOCKAITIS, KEITHANNE - Indiana University
item PODICHETI, RAM - Indiana University
item Tondo, Cecile
item SCHNELL, RAYMOND - Mars, Inc

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/15/2012
Publication Date: 1/15/2012
Citation: Kuhn, D.N., Liningstone Iii, D., Mockaitis, K., Podicheti, R., Tondo, C.L., Schnell, R.J. 2012. Design of an Illumina Infinium 6k SNPchip for genotyping two large avocado mapping populations. Meeting Abstract. Available: https://www.researchgate.net/publication/268120907.

Interpretive Summary: Two large mapping populations for avocado have been generated: a California mapping population of a reciprocal cross of ‘Hass’ and ‘Bacon’ (~1000 individuals) and a Florida mapping population of a reciprocal cross of ‘Simmonds’ and ‘Tonnage’ (~1000 individuals). To reduce the time and cost of genetic mapping using microsatellite markers, we have designed an Illumina Infinium chip comprising 6000 SNPs that represents 6000 individual loci. The SNP discovery process was completed by 454 sequencing ‘Hass’ RNA from leaves and flowers to create a reference transcriptome with 33,957 contigs. RNA from leaves and flowers of the parents (‘Hass’, ‘Bacon’, ‘Simmonds’ and ‘Tonnage’) was sequenced on the Illumina GAII platform, aligned to the reference transcriptome and 660,911 SNPs were identified. The SNPs were filtered through the following steps: removal of SNPs that had another SNP within 60 nucleotides, removal of SNPs within 50 nucleotides of an intron, retention of SNPs with Illumina quality (ADT) scores greater than 0.90, removal of SNPs from the same contig, selection of SNPs that were mappable in both populations (less than 6000), selection of SNPs mappable in at least one population (greater than ~15,000), selection of SNPs in single copy avocado genes. The chip now represents 6000 loci, 2,064 are mappable in both populations, 1,968 in only the Florida population, 1,968 in only the California population, and 3,297 that are in single copy genes. Collection of phenotypic data has begun on the Florida mapping population, such as cold tolerance, thrip damage, fruit weight, seed weight, number of fruits per tree, fruit size and diameter, fruit dry weight and oil content. Ranges of variation for some of these traits will be discussed. Our results are important to scientists researching important agronomic traits in avocado and to avocado breeders. These mapping populations will allow us to associate particular genetic markers with phenotypic traits such as cold tolerance, high oil content, fatty acid composition and flowering type. Development of such markers will provide breeders with a way to screen new seedlings for favorable alleles in an avocado breeding program. This will accelerate progress in breeding of new avocado varieties with improved disease resistance and nutritional qualities.

Technical Abstract: Two large mapping populations for avocado have been generated: a California mapping population of a reciprocal cross of ‘Hass’ and ‘Bacon’ (~1000 individuals) and a Florida mapping population of a reciprocal cross of ‘Simmonds’ and ‘Tonnage’ (~1000 individuals). To reduce the time and cost of genetic mapping using microsatellite markers, we have designed an Illumina Infinium chip comprising 6000 SNPs that represents 6000 individual loci. The SNP discovery process was completed by 454 sequencing ‘Hass’ RNA from leaves and flowers to create a reference transcriptome with 33,957 contigs. RNA from leaves and flowers of the parents (‘Hass’, ‘Bacon’, ‘Simmonds’ and ‘Tonnage’) was sequenced on the Illumina GAII platform, aligned to the reference transcriptome and 660,911 SNPs were identified. The SNPs were filtered through the following steps: removal of SNPs that had another SNP within 60 nucleotides, removal of SNPs within 50 nucleotides of an intron, retention of SNPs with Illumina quality (ADT) scores greater than 0.90, removal of SNPs from the same contig, selection of SNPs that were mappable in both populations (less than 6000), selection of SNPs mappable in at least one population (greater than ~15,000), selection of SNPs in single copy avocado genes. The chip now represents 6000 loci, 2,064 are mappable in both populations, 1,968 in only the Florida population, 1,968 in only the California population, and 3,297 that are in single copy genes. Collection of phenotypic data has begun on the Florida mapping population, such as cold tolerance, thrip damage, fruit weight, seed weight, number of fruits per tree, fruit size and diameter, fruit dry weight and oil content. Ranges of variation for some of these traits will be discussed.