Criteria for prioritizing selection of Mexican maize landrace accessions for conservation in situ or ex situ based on phylogenetic analysis

Abstract

Introduction: A combination of factors including migration, climate change and the encroachment of growing cities are associated with the extinction of species and a reduction in biodiversity. In Mexico maize landraces are an important source of germplasm that could be invaluable for future breeding programs in response a changing environment. Efforts to develop conservation strategies are hampered by the costs of housing and maintaining large germplasm collections. Effective criteria are therefore needed to identify rare genotypes that are in danger of being lost and to define minimal cost-effective core collections. Methods: A large-scale genotyping analysis of Mexican maize landraces was carried out using 14 SSR markers spread across the 10 maize chromosomes. DNA was extracted from 30 individual plants of each accession and 3 bulks containing 220ng of DNA from each of 10 individual plants were prepared. Amplification reactions were carried out individually on each bulk sample and SSRs were detected using an automatic sequencer. Binary scores were used to produce phylogenies and a rareness index Ri was developed to identify a minimal collection of accessions. Results: A total of 40,140 individual plants from accessions obtained in 14 different Mexican states and covering 47 maize races were analyzed. Accessions from Northern and Central-Southern states could be distinguished based on genotype and accessions from Michoacán state were found to be distinct to all other accessions. A minimal collection of 56 accessions that covered all identified alleles and included rare allele combinations was determined. Discussion: The strategy employed successfully distinguished accessions from different regions of Mexico and identified rare germplasm and offers a cost effective method to determine minimal germplasm collections for conservation in situ or ex situ. The strategy could easily be adapted for use in other native crop species such as common bean, chili pepper and tomato among others.