Search

Species misclassification (misidentification) and handling errors have been frequently reported in various plant species conserved at diverse gene banks, which could restrict use of germplasm for correct purpose. The objectives of the present study were to (i) determine the extent of genotyping error (reproducibility) on DArTseq-based single-nucleotide polymorphisms (SNPs); (ii) determine the proportion of misclassified accessions across 3134 samples representing three African rice species complex (Oryza glaberrima, O. barthii, and O. longistaminata) and an Asian rice (O. sativa), which are conserved at the AfricaRice gene bank; and (iii) develop species- and sub-species (ecotype)-specific diagnostic SNP markers for rapid and low-cost quality control (QC) analysis. Genotyping error estimated from 15 accessions, each replicated from 2 to 16 times, varied from 0.2 to 3.1%, with an overall average of 0.8%. Using a total of 3134 accessions genotyped with 31,739 SNPs, the proportion of misclassified samples was 3.1% (97 of the 3134 accessions). Excluding the 97 misclassified accessions, we identified a total of 332 diagnostic SNPs that clearly discriminated the three indigenous African species complex from Asian rice (156 SNPs), O. longistaminata accessions from both O. barthii and O. glaberrima (131 SNPs), and O. sativa spp. indica from O. sativa spp. japonica (45 SNPs). Using chromosomal position, minor allele frequency, and polymorphic information content as selection criteria, we recommended a subset of 24 to 36 of the 332 diagnostic SNPs for routine QC genotyping, which would be highly useful in determining the genetic identity of each species and correct human errors during routine gene bank operations. Electronic supplementary material The online version of this article (10.1007/s11032-018-0885-z) contains supplementary material, which is available to authorized users.

New Rice(s) for Africa (NERICA) are high yielding rice varieties mostly cultivated in Sub-Saharan Africa and developed by the Africa Rice Center. This study is aimed at investigating the proportion of introgression of parental genomic contribution of 60 lowland NERICA varieties and establishment of molecular profiling. Agro-morphological data from 17 characteristics was recorded and significant (ppOryza glaberrima) into 52 lowland NERICA lines (TOG5681 and IR64) as follows: 11% for BC2, 6.07% for BC3, and 7.55% for BC4. The introgression proportions for the eight remaining lowland NERICA lines derived from other crosses ranged from 5.5 to 11.3%. The proportion recorded with the recurrent parent was 83.99%. The highest introgression proportions of the O. glaberrima allele for all 60 lowland NERICA lines were found on chromosomes 2, 6 and 12 (TOG5681/IR64) and on chromosome 3 with NERIC-L-29 (TOG5681/IR1529-680-3-2). Multivariate analyses performed using an association of agro-morphological and molecular data revealed two major groups according to the distribution of the lowland NERICAs including the lowland NERICAs released were found in cluster 1 of the dendrogram. Genetic and genomic studies, QTL identification and analysis using agro-morphologically significant traits revealed should be used to develop mega-varieties adapted in rice growth conditions in Sub-Saharan Africa.

Bowman–Birk inhibitor (BBI) genes encode serine protease inhibitors well known for their anticarcinogenic properties and roles in plant defense against insects and pathogens. Here we investigated the expression of a BBI gene in response to water deficit, recovery and phytohormones. A full length cDNA encoding a novel BBI (AhBBI) was isolated from peanut (Arachis hypogaea L.) leaves. The deduced protein is a polypeptide of 11.5 kDa containing a signal peptide of 20 amino acids which is missing from peanut seed full-length BBI. Sequence analysis showed that AhBBI presents the characteristic features of BBIs but its first inhibitory loop is unique among the Fabaceae species. Real-time PCR analyses indicated that in peanut leaves, AhBBI is upregulated by water deficit and exogenous jasmonic acid (JA) but repressed by abscissic acid (ABA) after 24 h of treatment. The transcripts accumulation patterns during water deficit differed between two cultivars studied in relation to their tolerance levels to drought. AhBBI transcripts accumulated earlier and stronger in the tolerant cultivar (cv. Fleur11) compared to the susceptible one (cv. 73–30) suggesting that BBI genes are involved in drought stress tolerance. Subsequent rehydration reversed the accumulation of AhBBI transcripts in both cultivars but at different levels. The overall role of BBI in abiotic stress tolerance and the possible mechanisms of action are discussed.

Peanut (Arachis hypogaea L.) is an important subsistence and cash crop in the semi-arid tropics where it often suffers from drought stress. Although its ecophysiological responses are studied, little is known about the molecular events involved in its adaptive responses to drought. The aim of this study was to investigate the involvement of membrane phospholipid and protein degrading enzymes as well as protective proteins such as "late embryogenesis-abundant" (LEA) protein in peanut adaptive responses to drought. Partial cDNAs encoding putative phospholipase Da, cysteine protease, serine protease and a full-length cDNA encoding a LEA protein were cloned. Their expression in response to progressive water deficit and rehydration was compared between cultivars differing in their tolerance to drought. Differential gene expression pattern ac-cording to either water deficit intensity and cultivar's tolerance to drought were observed. A good correspondence between the molecular responses of the studied cultivars and their physiological responses previously defined in greenhouse and field experiments was found. Molecular characters, as they were detectable at an early stage, could therefore be efficiently integrated in groundnut breeding programmes for drought adaptation. Thus, the relevance of the target genes as drought tolerance indicators is discussed. © 2007 Elsevier Masson SAS. All rights reserved.