Genetic variation and structure of maize populations from Saoura and Gourara oasis in Algerian Sahara

Abstract

BackgroundThe ability of maize populations/landraces to tolerate drastically extreme environments over the past four centuries in Algeria leads to characterize these genetic resources for germplasm management as well as the identification of the best landraces useful for genetic improvement. Thus, the aim of the present work was a fingerprinting of an Algerian maize collection (47 landraces) from Saharan oasis by using 24 agro-morphological traits and18 Simple Sequence Repeats to evaluate genetic diversity and population structure.ResultsPhenotypic traits showed large significant variation in which earliness, plant size, ear and kernel features and crop yield appeared the most discriminant traits among landraces by using principal component analysis (PCA). One hundred ninety-seven different alleles were detected with a high mean number of allele per locus (10.9). The selected SSR were highly informative with PIC values > 0.65 as well as an overall genetic diversity (0.47) highlighting a broad genetic variability in the analyzed landraces. Genetic structure analysis revealed a high genetic differentiation among the 47 maize landraces with an overall Fst value (0.33). Cluster analysis for morphological traits as well as for SSR markers grouped the 47 Algerian populations regardless their geographic origin.ConclusionsMaize from Algerian desert harbors a wide genetic diversity offering a source of novel/unique alleles useful for maize breeding programs to face the ongoing and future major challenge, the climate changes.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0655-2) contains supplementary material, which is available to authorized users.

Genomic Analysis of Selected Maize Landraces from Sahel and Coastal West Africa Reveals Their Variability and Potential for Genetic Enhancement

“…Further, the low variation in the genetic indices identified between the landraces as a group, and the reference populations showed that the two germplasm sets possessed similar genetic diversity ( Table 1 ). These results agreed with previous findings that tropical maize germplasm is highly diverse with H e > 0.3 [ 37 , 38 , 39 ]. The mean PIC obtained in the present study, 0.29 using 5974 DArTseq SNPs for the 208 maize accessions was higher than the 0.19 and 0.26 reported for tropical early-maturing maize inbred lines using 15,047 [ 30 ] and 7224 SNPs for a sample size of 94 and 134, respectively [ 20 , 27 ].…”

Genetic characterization and divergence studies of maize (Zea maysL.) lines developed from landraces indigenous to North Eastern Hill Region (NEHR) of India

“…The allelic richness of these landraces are yet to be explored to their full potential (Singode and Prasanna, 2010) and the current study to characterize inbreds developed from the indigenous landraces of NEHR was one such attempt. Genetic divergence studies help to define breeding strategies geared to address challenges of yield and an understanding of the same is a prerequisite for exploitation of heterosis (Yao et al, 2007;Semagn et al, 2012;Aci et al, 2018). For the current subset, a significant increase in percent homozygosity ranging between 70 and 100% as against the expected theoretical average of approximately 88% (Hallauer et al, 2010) on account of inbreeding leading to a deviation from Hardy-Weinberg expectations were observed.…”

Divergence among maize genotypes with different kernel types according to SSR marker analysis

“…Primer sequences are available at the MaizeGDBwebsite (https://www.maizegdb.org/data_center/ssr) and their characteristics are given in Table 2. Also, we tried to include as little as possible markers with dinucleotide repeats (28.6%), considering the fact that they produce stuttering bands, which is not the case with the markers with other types of repeats as stated in many previous publications (IGNJATOVIC-MICIC et al, 2015;ACI et al, 2018). Total volume of each PCR reaction was 25 µl and final concetrations of components were as follows: 1 x buffer, 0.5 µM primers, 0.8 mM dNTPs each, 1 U of Taq Polymerase (Thermo Scientific), 2 µl of 25 µg/µl genomic DNA and sterile water.…”