Genome-wide SNP genotyping of DNA pools identifies untapped landraces and genomic regions that could enrich the maize breeding pool

Abstract

Maize landraces preserved in genebanks have a large genetic diversity that is still poorly characterized and underexploited in modern breeding programs. Here, we genotyped DNA pools from 156 American and European landraces with a 50K SNP Illumina array to study the effect of both human selection and environmental adaptation on the genome-wide diversity of maize landraces. Genomic diversity of landraces varied strongly in different parts of the genome and with geographic origin. We detected selective footprints between landraces of different geographic origin in genes involved in the starch pathway (Su1, Waxy1), flowering time (Zcn8, Vgt3, ZmCCT9) and tolerance to abiotic and biotic stress (ZmASR, NAC and dkg genes). Landrace diversity was compared to that of (i) 327 inbred lines representing American and European diversity (″CK lines″) and (ii) 103 new lines derived directly from landraces (″DH-SSD lines″). We observed limited diversity loss or selective sweep between landraces and CK lines, except in peri-centromeric regions. However, analysis of modified Roger′s distance between landraces and the CK lines showed that most landraces were not closely related to CK lines. Assignment of CK lines to landraces using supervised analysis showed that only a few landraces, such as Reid′s Yellow Dent, Lancaster Surecrop and Lacaune, strongly contributed to modern European and American breeding pools. Haplotype diversity of CK lines was more enriched by DH-SSD lines that derived from the landraces with no related lines and the lowest contribution to CK lines. Our approach opens an avenue for the identification of promising landraces for pre-breeding.

Multifaceted Analysis of Barley Landraces Collected during Gene Bank Expeditions in Poland at the End of the 20th Century

“…The chances of their use are increased by the direct deriving of homozygous lines by single seed descent and providing detailed information on their genotype and phenotype. The effectiveness of such an approach has been demonstrated for example for wheat or maize [44][45][46].…”

Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array

“…Using residual heterozygosity to calibrate model is not possible since half SNPs show no heterozygous genotype in the 327 inbred lines of our study. Obtaining at least 16 heterozygous individuals for each SNP therefore requires to genotype a few dozens of F1 hybrids or individuals from landraces considering that expected heterozygosity in a landrace is comprised between 3 and 28% ( Arca et al, 2020 ). This represents additional costs since maize researchers and breeders genotyped preferentially inbred lines to access directly haplotypes without phasing and because genotypes of F1 hybrids can be deduced of that of their parental inbred lines.…”

“…The DNA pooling approach we propose overcomes specific issues for genetic diversity analysis and plant germplasm management purposes that were not or partially addressed by previous methods which were mostly focused on QTL analysis and genome wide association studies ( Hoogendoorn et al, 2000 ; Brohede et al, 2005 ; Craig et al, 2005 ; Teumer et al, 2013 ). As proof of concept, we used the DNA pooling approach to estimate allelic frequencies in maize landraces in order to identify original maize landraces in germplasm for pre-breeding purposes and selective footprints between geographic and/or admixture groups of landraces cultivated in contrasted agro-climatic conditions ( Arca et al, 2020 ). Our approach could be very interesting for studying plant germplasm since time, money and molecular skills can be limiting factors to study and compare large collections of landraces maintained in seedbank ( Mir et al, 2013 ; Diaw et al, 2020 ).…”

“…Genotyping DNA bulks of individuals from landraces with SNP arrays could therefore be interesting to characterize and manage genetic diversity in plant germplasm. SNP arrays could be notably a valuable tool to identify selective sweep between landraces depending on their origin, to manage plant germplasm collection at worldwide level (e.g., identify duplicate), to identify landraces poorly used so far in breeding programs or to identify genomic regions where diversity has been lost during the transition from landraces to inbred lines ( Arca et al, 2020 ).…”

“…Additionally, calibration of equations for predicting allelic frequencies of DNA bulks for each SNP is based on controlled pools with variable allelic frequencies rather than only heterozygous genotypes as in previous methods ( Hoogendoorn et al, 2000 ; Brohede et al, 2005 ; Peiris et al, 2011 ; Teumer et al, 2013 ). As a proof of concept, we applied our new approach to maize by estimating allelic frequencies of 23,412 SNPs in 156 maize landraces representative of European and American diversity present in genebanks ( Arca et al, 2020 ). To our knowledge, it is the first time that a DNA bulk approach was used on 50K maize high-throughput SNP array to study genetic diversity within maize landraces germplasm.…”