An SSR‐based approach incorporating a novel algorithm for identification of rare maize genotypes facilitates criteria for landrace conservation in Mexico

Abstract

As maize was domesticated in Mexico around 9,000 years ago, local farmers have selected and maintained seed stocks with particular traits and adapted to local conditions. In the present day, many of these landraces are still cultivated; however, increased urbanization and migration from rural areas implies a risk that this invaluable maize germplasm may be lost. In order to implement an efficient mechanism of conservation in situ, the diversity of these landrace populations must be estimated. Development of a method to select the minimum number of samples that would include the maximum number of alleles and identify germplasm harboring rare combinations of particular alleles will also safeguard the efficient ex‐situ conservation of this germplasm. To reach this goal, a strategy based on SSR analysis and a novel algorithm to define a minimum collection and rare genotypes using landrace populations from Puebla State, Mexico, was developed as a “proof of concept” for methodology that could be extended to all maize landrace populations in Mexico and eventually to other native crops. The SSR‐based strategy using bulked DNA samples allows rapid processing of large numbers of samples and can be set up in most laboratories equipped for basic molecular biology. Therefore, continuous monitoring of landrace populations locally could easily be carried out. This methodology can now be applied to support incentives for small farmers for the in situ conservation of these traditional cultivars.

An informational view of accession rarity and allele specificity in germplasm banks for management and conservation

“…Nonetheless, as predicted by the theory, the average accession rarity was exactly equal to the average accession divergence. The use of rarity, defined by Eq (3) , has a fundamental difference with divergence, defined by Eq (4) : while rarity considers the allele distribution across all accessions, divergence is only based on the allele frequencies of the given accession and the average of the collection, which is the same case of the use of the square euclidean distance [ 9 ].…”

“…Since an accession forms part of a genetic continuum in a collection, the frequency-based definition of the rarity of a biological species, a rather discrete unit in the tree of life, does not apply to the entries of a seed bank. To the best of our knwledge, only one definition of the rarity of an accession, based on marker data, has been proposed, in the context of application to SSR maize data [ 9 ]. It is basically the square euclidean distance between the array of allele frequencies in a given accession, and the average frequencies for the whole collection.…”

Development of nuclear microsatellite markers to facilitate germplasm conservation and population genetics studies of five groups of tropical perennial plants with edible fruits and shoots: rambutan (Nephelium lappaceum L.), sapodilla (Manilkara zapota (L.) P. Royen), lychee (Litchi chinensis Sonn.), mangosteen (Garcinia mangostana Linn. and Garcinia cochinchinensis (Lour.) Choisy) and bamboo (Bambusa vulgaris Schrad. ex J.C. Wendl and Guadua angustifolia Kunth)

“…Also, 46 polymorphic SSRs were used to analyze the genetic structure of mango cultivars from around the world, conservation of germplasm and to facilitate the use of genetic resources for breeding purposes (Yamanaka et al 2019). Even in current times when genotyping by sequencing (GBS) has become inexpensive, SSRs are still the preferred effective, robust, reproducible and simple to use tool to determine genetic diversity of landraces of maize and preserve rare allele sources; as SSRs do not require large bioinformatics infrastructure and expertise for data analysis (Hayano-Kanashiro et al 2017).…”

Wild plant conservation in Mexico in the 21st century

“…Since then, milestones of the outmost importance have been reached in terms of integrating and analyzing information from different disciplines such as taxonomy, ecology, physiology, agronomy, geography, climatology, edaphology, and even from the social sciences to define both general and particular approaches to the biological conservation, as well as the use of technologies that are necessary to support increasingly robust conservation proposals (e.g., Bojórquez-Tapia et al 1995, Álvarez-Buylla et al 1996, Heywood & Iriondo 2003, Heywood & Dulloo, 2005, Lascuráin et al 2009, Costedoat et al 2015, Brooks et al 2016, Larkin et al 2016, Hayano-Kanashiro et al 2017, List et al 2017, Pfaff et al 2017.…”