Development of genomic microsatellites in Gleditsia triacanthos (Fabaceae) using Illumina sequencing

Abstract

• Premise of the study: Fourteen genomic microsatellite markers were developed and characterized in honey locust, Gleditsia triacanthos, using Illumina sequencing. Due to their high variability, these markers can be applied in analyses of genetic diversity and structure, and in mating system and gene flow studies.• Methods and Results: Thirty-six individuals from across the species range were included in a genetic diversity analysis and yielded three to 20 alleles per locus. Observed heterozygosity and expected heterozygosity ranged from 0.214 to 0.944 and from 0.400 to 0.934, respectively, with minimal occurrence of null alleles. Regular segregation of maternal alleles was observed at seven loci and moderate segregation distortion at four of 11 loci that were heterozygous in the seed parent.• Conclusions: Honey locust is an important agroforestry tree capable of very fast growth and tolerance of poor site conditions. This is the first report of genomic microsatellites for this species.

Development of genic and genomic microsatellites in Gleditsia triacanthos L. (Fabaceae) using Illumina sequencing

“…For genomic SSR development, Illumina low-coverage genome sequencing was used to generate 14,888,028 paired-end sequences assembled into 13,775,803 contigs in a size range from 93-191 bp (Owusu et al 2013, Staton et al 2015. A total of 4715 primer pairs flanking SSR motifs were identified (Owusu et al 2013).…”

“…It is a member of the subfamily Caesalpinioideae, for which only a limited number of markers and other genomic resources are available (La Malfa et al 2014, Gailing et al 2017. The transfer of genic microsatellites (Expressed Sequence Tag-Simple Sequence Repeats (EST-SSRs)) developed for the related species Ceratonia siliqua L. (La Malfa et al 2014) to honeylocust was not successful (Owusu et al 2013). Earlier, we developed 14 genomic SSRs in honeylocust using low-coverage whole genome sequencing (Owusu et al 2013).…”

“…The transfer of genic microsatellites (Expressed Sequence Tag-Simple Sequence Repeats (EST-SSRs)) developed for the related species Ceratonia siliqua L. (La Malfa et al 2014) to honeylocust was not successful (Owusu et al 2013). Earlier, we developed 14 genomic SSRs in honeylocust using low-coverage whole genome sequencing (Owusu et al 2013). All of these markers were applicable for genetic variation assessments in a reference panel of 36 samples collected from a provenance trial (Owusu et al 2013).…”

“…Earlier, we developed 14 genomic SSRs in honeylocust using low-coverage whole genome sequencing (Owusu et al 2013). All of these markers were applicable for genetic variation assessments in a reference panel of 36 samples collected from a provenance trial (Owusu et al 2013). However, due to signatures of null alleles in some seed parents, only six to nine of these markers were used for gene flow analyses in honeylocust population fragments (Owusu et al 2016).…”

“…While we have already developed a limited number of non-genic microsatellite markers for honeylocust (Owusu et al 2013), no transcriptome resources and gene-based markers such as EST-SSRs have been published for this species. The development of transcriptome resources such as stress-induced transcriptome libraries is especially important since hardwood species including honeylocust are increasingly threatened by abiotic stresses such as drought and heat, especially at their southern distribution edge.…”