Screening African rice (Oryza glaberrima) for tolerance to abiotic stresses: I. Fe toxicity

AbstractIron (Fe) toxicity is recognized as one of the most widely spread soil constraints for rice production especially in West Africa. Oryza glaberrima the cultivated rice species that originated from West Africa is well-adapted to its growing ecologies. The aim of this study was to identify the promising O. glaberrima accessions tolerant to Fe toxicity from the 2106 accessions held at the AfricaRice gene bank. The screenings were conducted over a four-year period and involved evaluating the entries under Fe-toxic field conditions in West Africa, selecting good yielding accessions and repeating the testing with newly selected lines. Three accessions (TOG 7206, TOG 6218-B and TOG 7250-A) were higher yielding than O. sativa checks under stress but with similar yields under control conditions. These accessions yielded over 300g/m2 under both Fe toxicity and control conditions. In conclusion, these materials could be used as donors in breeding programs for developing high yielding rice varieties suited to Fe toxicity affected areas in West Africa

Development of species diagnostic SNP markers for quality control genotyping in four rice (Oryza L.) species

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

Cloning, characterization and differential expression of a Bowman–Birk inhibitor during progressive water deficit and subsequent recovery in peanut (Arachis hypogaea) leaves

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

A novel allele of the P‑starvation tolerance gene OsPSTOL1 from African rice (Oryza glaberrima Steud) and its distribution in the genus Oryza

We have developed allele-specific markers for molecular breeding to transfer the PSTOL1 gene from Kasalath to African mega-varieties, including NERICAs, to improve their tolerance to P-deficient soil. The deficiency of phosphorus (P) in soil is a major problem in Sub-Saharan Africa due to general nutrient depletion and the presence of P-fixing soils. Developing rice cultivars with enhanced P efficiency would, therefore, represent a sustainable strategy to improve the livelihood of resource-poor farmers. Recently the Pup1 locus, a major QTL for tolerance to P deficiency in soil, was successfully narrowed-down to a major gene, the protein kinase OsPSTOL1 (P-starvation tolerance), which was found to be generally absent from modern irrigated rice varieties. Our target is to improve the tolerance of African mega-varieties to P deficiency through marker-assisted introgression of PSTOL1. As a first step, we have determined the Pup1 haplotype and surveyed the presence or absence of PSTOL1 and other genes of the Pup1 locus in African mega-varieties, NERICAs (New Rice for Africa) and their Oryza glaberrima parents. Here, we report the presence of a novel PSTOL1 allele in upland NERICAs that was inherited from the O. glaberrima parent CG14. This allele showed a 35 base-pair substitution when aligned to the Kasalath allele, but maintained a fully conserved kinase domain, and is present in most O. glaberrima accessions evaluated. In-silico and marker analysis indicated that many other genes of the Kasalath Pup1 locus were missing in the O. glaberrima genome, including the dirigent-like gene OsPupK20-2, which was shown to be downstream of PSTOL1. We have developed several allele-specific markers for the use for molecular breeding to transfer the PSTOL1 gene from Kasalath to African mega-varieties, including NERICAs

Multienvironment Quantitative Trait Loci Mapping and Consistency across Environments of Resistance mechanisms to Ferrous Iron Toxicity in Rice

Analysis of 33 varieties of three sorghum (Sorghum spp.) species cultivated in China showed that sudangrass (Sorghum sudanense Stapf) and sorghum–sudangrass hybrid [Sorghum bicolor (L.) Moench × S. sudanense] samples had higher concentrations of phenolic compounds (including total soluble phenol, proanthocyanidin, flavan-4-ols, anthocyanins, and five phenolic acids) than sorghum (S. bicolor) samples. In addition, the phenolic compounds were distributed extensively in the grain morphological fractions (including glumes, spikelets, caryopsis, endosperm, and embryo) of sudangrass and sorghum–sudangrass hybrid samples; however, they were mainly present in the glumes of sorghum except for total soluble phenol. The results indicated that sudangrass and sorghum–sudangrass hybrid samples in this study would be good sources of useful phenolic compounds such as anthocyanin (6.93 mg g−1 and 4.72 mg g−1) and proanthocyanidin (10.37 mg g−1 and 8.16 mg g−1) compared with sorghum samples (2.97 mg g−1 and 0.18 mg g−1 for anthocyanin and proanthocyanidin, respectively). Sudangrass and sorghum–sudangrass hybrid samples had higher antioxidant activities of 2,2¢-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) and 1,1-diphenyl-2-picrylhydrazyl radical (DPPH) (230 and 108 μmol trolox equivalents [TE] g−1 for sudangrass; 258.5 and 130.3 μmol TE g−1 for sorghum–sudangrass hybrid) than sorghum samples (202.5 and 39.5 μmol TE g−1 for ABTS and DPPH, respectively). Thus, the sudangrass and sorghum–sudangrass hybrid samples in this study represented better commercial resources for nutritional and pharmaceutical purposes than sorghum samples because of higher antioxidant activities

Screening African rice (Oryza glaberrima) for tolerance to abiotic stresses: I. Fe toxicity.

Iron (Fe) toxicity is recognized as one of the most widely spread soil constraints for rice production especially in West Africa. Oryza glaberrima the cultivated rice species that originated from West Africa is well-adapted to its growing ecologies. The aim of this study was to identify the promising O. glaberrima accessions tolerant to Fe toxicity from the 2106 accessions held at the AfricaRice gene bank. The screenings were conducted over a four-year period and involved evaluating the entries under Fe-toxic field conditions in West Africa, selecting good yielding accessions and repeating the testing with newly selected lines. Three accessions (TOG 7206, TOG 6218-B and TOG 7250-A) were higher yielding than O. sativa checks under stress but with similar yields under control conditions. These accessions yielded over 300 g/m2 under both Fe toxicity and control conditions. In conclusion, these materials could be used as donors in breeding programs for developing high yielding rice varieties suited to Fe toxicity affected areas in West Africa