Genetic Diversity in maize landraces from Southern South America: new insights from genotyping-by-sequencing.

LOPEZ, M. G.; FILIPPI, C.V.; PUEBLA, A.F.; FASS, MÓNICA I.; PANIEGO, N.B.; HOPP, H.E.; LIA, V.V.

Simposio; Third International Harlan Symposium; 2019

Native maize landraces are a valuable reservoir of original alleles for crop improvement. In Argentina these resources are maintained by traditional farmers, who descended from indigenous populations. Nowadays, local landraces are threatened by the mixing with commercial hybrids and the replacement of native varieties by more productive crops. Knowledge of the levels and distribution patterns of genetic variation in traditional landraces is essential in order to make proper decisions for conservation and to develop successful protection programs. Previous studies have detected significant genetic structuring between maize landraces from North West (NWA) and East (NEA) Argentina using microsatellite markers. However, additional information is still needed to clarify the origin of the Argentinean native germplasm and establish the focus of future conservation efforts. In the present work, we used double digest restriction‐site‐associated DNA (ddRAD) sequencing to further explore diversity patterns and population structure in maize landraces from Northern Argentina. A set of individuals representative of the previously identified genetic groups were genotyped using a combination of PstI and EcoRI restriction enzymes, with a size selection of 550-750 bp. Illumina sequencing data were processed using a custom pipeline. Single nucleotide polymorphisms (SNPs) were called using Stacks. A total of 26633 putative SNPs were identified after initial filtering with Stacks. Of these, 4614 SNPs remained after considering linkage disequilibrium, paralogous sequence variants and percentage of missing data. Estimates of genetic variability were moderate. Patterns of population structure were similar to those of past studies, with a clear distinction between highland and lowland landraces. A new lowland subgroup was detected for NWA. The availability of genome-wide SNP markers for Argentinian landraces will allow to better inform conservation strategies and will provide valuable tools to investigate the genetic basis of local adaptation.