Genetic diversity and selection signatures in maize landraces compared across 50 years of in situ and ex situ conservation

Abstract

Genomics-based, longitudinal comparisons between ex situ and in situ agrobiodiversity conservation strategies can contribute to a better understanding of their underlying effects. However, landrace designations, ambiguous common names, and gaps in sampling information complicate the identification of matching ex situ and in situ seed lots. Here we report a 50-year longitudinal comparison of the genetic diversity of a set of 13 accessions from the state of Morelos, Mexico, conserved ex situ since 1967 and retrieved in situ from the same donor families in 2017. We interviewed farmer families who donated in situ landraces to understand their germplasm selection criteria. Samples were genotyped by sequencing, producing 74,739 SNPs. Comparing the two sample groups, we show that ex situ and in situ genome-wide diversity was similar. In situ samples had 3.1% fewer SNPs and lower pairwise genetic distances (Fst 0.008–0.113) than ex situ samples (Fst 0.031–0.128), but displayed the same heterozygosity. Despite genome-wide similarities across samples, we could identify several loci under selection when comparing in situ and ex situ seed lots, suggesting ongoing evolution in farmer fields. Eight loci in chromosomes 3, 5, 6, and 10 showed evidence of selection in situ that could be related with farmers’ selection criteria surveyed with focus groups and interviews at the sampling site in 2017, including wider kernels and larger ear size. Our results have implications for ex situ collection resampling strategies and the in situ conservation of threatened landraces.

Genome-wide diversity in lowland and highland maize landraces from southern South America: population genetics insights to assist conservation

“…To quantify adaptive differences, outlier detection methods come into play by identifying loci characterised by high genetic differentiation relative to the overall population structure, indicative of their likely involvement in divergent selection. The identification of selection signatures at multiple SNPs in the comparative analysis between HNWA and FNEA (Figure 5B), coupled with compelling evidence of local adaptation within Mexican and other South American maize landraces (Gates et al, 2019; McLean-Rodríguez et al, 2021; Wang et al, 2021; Janzen et al, 2022), suggests that these two groups exhibit signs of local adaptation.…”

Genomic prediction of tocochromanols in exotic‐derived maize

“…The diverse germplasm available from gene banks and exotic‐derived panels, such as the BGEM panel studied here, are a critical resource for breeders, especially as they continue to improve both yield and nutritional content in the face of rapid changes in climate coupled with increasing global population (Dyer et al., 2014; McLean‐Rodríguez et al., 2021; Vanous et al., 2018; Yu et al., 2016). Notably, exotic donor lines have already been used to increase provitamin A in maize grain (Menkir et al., 2015).…”

Advances in identifying GM plants: toward the routine detection of ‘hidden’ and ‘new’ GMOs

“…The repeated traditional selection over 10 000 years has left selection signatures of human pressures in the peasants' landraces and the companies' cultivars (McLean-Rodríguez et al, 2021).…”