Development and Genetic Characterization of Peanut Advanced Backcross Lines That Incorporate Root-Knot Nematode Resistance From Arachis stenosperma

Crop wild species are increasingly important for crop improvement. Peanut (Arachis hypogaea L.) wild relatives comprise a diverse genetic pool that is being used to broaden its narrow genetic base. Peanut is an allotetraploid species extremely susceptible to peanut root-knot nematode (PRKN) Meloidogyne arenaria. Current resistant cultivars rely on a single introgression for PRKN resistance incorporated from the wild relative Arachis cardenasii, which could be overcome as a result of the emergence of virulent nematode populations. Therefore, new sources of resistance may be needed. Near-immunity has been found in the peanut wild relative Arachis stenosperma. The two loci controlling the resistance, present on chromosomes A02 and A09, have been validated in tetraploid lines and have been shown to reduce nematode reproduction by up to 98%. To incorporate these new resistance QTL into cultivated peanut, we used a marker-assisted backcrossing approach, using PRKN A. stenosperma-derived resistant lines as donor parents. Four cycles of backcrossing were completed, and SNP assays linked to the QTL were used for foreground selection. In each backcross generation seed weight, length, and width were measured, and based on a statistical analysis we observed that only one generation of backcrossing was required to recover the elite peanut’s seed size. A populating of 271 BC3F1 lines was genome-wide genotyped to characterize the introgressions across the genome. Phenotypic information for leaf spot incidence and domestication traits (seed size, fertility, plant architecture, and flower color) were recorded. Correlations between the wild introgressions in different chromosomes and the phenotypic data allowed us to identify candidate regions controlling these domestication traits. Finally, PRKN resistance was validated in BC3F3 lines. We observed that the QTL in A02 and/or large introgression in A09 are needed for resistance. This present work represents an important step toward the development of new high-yielding and nematode-resistant peanut cultivars.

Accumulating candidate genes for broad-spectrum resistance to rice blast in a drought-tolerant rice cultivar

Biotic stresses, including diseases, severely affect rice production, compromising producers’ ability to meet increasing global consumption. Understanding quantitative responses for resistance to diverse pathogens can guide development of reliable molecular markers, which, combined with advanced backcross populations, can accelerate the production of more resistant varieties. A candidate gene (CG) approach was used to accumulate different disease QTL from Moroberekan, a blast-resistant rice variety, into Vandana, a drought-tolerant variety. The advanced backcross progeny were evaluated for resistance to blast and tolerance to drought at five sites in India and the Philippines. Gene-based markers were designed to determine introgression of Moroberekan alleles for 11 CGs into the progeny. Six CGs, coding for chitinase, HSP90, oxalate oxidase, germin-like proteins, peroxidase and thaumatin-like protein, and 21 SSR markers were significantly associated with resistance to blast across screening sites. Multiple lines with different combinations, classes and numbers of CGs were associated with significant levels of race non-specific resistance to rice blast and sheath blight. Overall, the level of resistance effective in multiple locations was proportional to the number of CG alleles accumulated in advanced breeding lines. These disease resistant lines maintained tolerance to drought stress at the reproductive stage under blast disease pressure.

Identification and Fine Mapping of qPBR10-1, A Novel Locus Controlling Panicle Blast Resistance in Pigm-Containing P/TGMS Line

Rice blast is one of the most widespread and devastating diseases in rice production. Tremendous success has been achieved in identification and characterization of genes and quantitative trait loci (QTLs) conferring seedling blast resistance, however, genetic studies on panicle blast resistance have lagged far behind. In this study, two advanced backcross inbred sister lines (MSJ13 and MSJ18) were obtained in the process of introducing Pigm into C134S, and showed significant differences in the panicle blast resistance. One F2 population derived from the crossing MSJ13/MSJ18 was used to QTL mapping for panicle blast resistance using Genotyping by Sequencing (GBS) method. A total of 7 QTLs were identified, including a major QTL qPBR10-1 on chromosome 10 that explaining 24.21% of phenotypic variance with LOD scores of 6.62. Furthermore, qPBR10-1 was verified via the BC1F2 and BC1F3 population and narrowed to a 60.6-kb region with six candidate genes predicted, including two genes encoding exonuclease family protein, two genes encoding hypothetical protein, and two genes encoding transposon protein. The nucleotide variations and the expression patterns of the candidate genes were identified and analyzed between MSJ13 and MSJ18 through sequence comparison and RT-PCR approach, and results indicated that ORF1 and ORF2 encoding exonuclease family protein might be the causal candidate genes for panicle blast resistance in the qPBR10-1 locus.

Genetic Mapping Reveals Novel Exotic and Elite QTL Alleles for Salinity Tolerance in Barley

Soil salinity is one of the constraints of crop production in Egypt. The aims of this study were to identify genomic regions associated with grain weight and its related traits along with their salinity tolerance indices and to identify the most salinity tolerant and high-yielding genotypes. Therefore, we evaluated an advanced backcross mapping population of barley in newly reclaimed soil under two salinity levels of groundwater aquifers in South of Sinai, Egypt. We detected significant QTL associated with grain weight related attributes and the salinity tolerance index (STI) distributed throughout the whole genome of barley, which can be used to enhance salinity tolerance. Moreover, the markers bPb-3739 (4H, 96.3 cM), AF043094A (5H, 156 cM), bPb-8161 (7H, 2.22 cM), and bPb-5260 (7H, 115.6 cM), were the most important identified genomic regions corresponding to vernalization, dwarfing and dehydrin genes, which are correlated with salinity tolerance. Additionally, the doubled haploid lines SI001, SI043, SI044, SI028, SI242, SI035, and SI005 had the highest STI values based on yield average. The present study demonstrated that wild and elite barley do harbor novel valuable alleles, which can enrich the genetic basis of cultivated barley and improve quantitative agronomic traits under salinity conditions.

Identification and fine mapping of qPBR10-1, a novel locus controlling panicle blast resistance in Pigm-containing P/TGMS line

Background Rice blast is one of the most widespread and devastating diseases in rice production. Tremendous success has been achieved in identification and characterization of genes and quantitative trait loci (QTLs) conferring seedling blast resistance, however, genetic studies on panicle blast resistance have lagged far behind. Results In this study, two advanced backcross inbred sister lines (MSJ13 and MSJ18) were obtained in the process of introducing Pigm into C134S, and showed significant differences in the panicle blast resistance. One F2 population derived from the crossing MSJ13/MSJ18 was used to QTL mapping for panicle blast resistance using Genotyping by Sequencing (GBS) method. A total of 7 QTLs were identified, including a major QTL qPBR10-1 on chromosome 10 that explaining 24.21% of phenotypic variance with LOD scores of 6.62. Furthermore, qPBR10-1 was verified via the BC1F2 and BC1F3 population and narrowed to a 60.6-kb region with six candidate genes predicted, including two genes encoding exonuclease family protein, two genes encoding hypothetical protein, and two genes encoding transposon protein. The nucleotide variations and the expression patterns of the candidate genes were identified and analyzed between MSJ13 and MSJ18 through sequence comparison and RT-PCR approach, and results indicated that ORF1 and ORF2 encoding exonuclease family protein might be the causal candidate genes for panicle blast resistance in the qPBR10-1 locus. Conclusions A total of 7 QTLs conferring panicle blast resistance was identified from one F2 population derived from the crossing between two advanced backcross inbred sister lines MSJ13 and MSJ18, which harbored the broad-spectrum resistance gene Pigm. A major QTL qPBR10-1 was fine mapped in a 60.6-kb region with six candidate genes predicted, and ORF1 and ORF2 encoding exonuclease family protein might be the causal candidate genes for panicle blast resistance in the qPBR10-1 locus through sequence comparison and RT-PCR approach.

Evaluation and Selection of Interspecific Lines of Groundnut (Arachis hypogaea L.) for Resistance to Leaf Spot Disease and for Yield Improvement

Early and late leaf spot are two devastating diseases of peanut (Arachis hypogaea L.) worldwide. The development of a fertile, cross-compatible synthetic amphidiploid, TxAG-6 ([A. batizocoi × (A. cardenasii × A. diogoi)]4x), opened novel opportunities for the introgression of wild alleles for disease and pest resistance into commercial cultivars. Twenty-seven interspecific lines selected from prior evaluation of an advanced backcross population were evaluated for resistance to early and late leaf spot, and for yield in two locations in Ghana in 2006 and 2007. Several interspecific lines had early leaf spot scores significantly lower than the susceptible parent, indicating that resistance to leaf spot had been successfully introgressed and retained after three cycles of backcrossing. Time to appearance of early leaf spot symptoms was less in the introgression lines than in susceptible check cultivars, but the opposite was true for late leaf spot. Selected lines from families 43-08, 43-09, 50-04, and 60-02 had significantly reduced leaf spot scores, while lines from families 43-09, 44-10, and 63-06 had high pod yields. One line combined both resistance to leaf spot and high pod yield, and several other useful lines were also identified. Results suggest that it is possible to break linkage drag for low yield that accompanies resistance. However, results also suggest that resistance was diluted in many of the breeding lines, likely a result of the multigenic nature of resistance. Future QTL analysis may be useful to identify alleles for resistance and allow recombination and pyramiding of resistance alleles while reducing linkage drag.

An advanced lentil backcross population developed from a cross between Lens culinaris × L. ervoides for future disease resistance and genomic studies

Genetically accessible variation to some of the abiotic and biotic stresses are limited in the cultivated lentil (Lens culinaris Medik.) germplasm. Introgression of novel alleles from its wild relative species will be useful for enhancing the genetic improvement of the crop. L. ervoides, one of the wild relatives of lentil, is a proven source of disease resistance for the crop. Here we introduce a lentil advanced backcross (LABC-01) population developed in cultivar ‘CDC Redberry’ background, based on L. ervoides alleles derived from an interspecific recombinant inbred population, LR-59-81. Two-hundred and seventeen individuals of the LABC-01 population at BC2F3:4 generation were screened for the race 0 of anthracnose (Colletotrichum lentis) and stemphylium blight (Stemphylium botryosum) under controlled conditions. The population showed significant variations for both diseases and the transfer of resistance alleles into the elite cultivar was evident. It also segregated for other traits such as days to flowering, seed coat colour, seed coat pattern and flower colour. Overall, we showed that LABC-01 population can be used in breeding programmes worldwide to improve disease resistance and will be available as a valuable genetic resource for future genetic analysis of desired loci introgressed from L. ervoides.

Importance of correcting genomic relationships in single-locus QTL mapping model with an Advanced Backcross population

Advanced Backcross (AB) populations have been widely used to identify and utilize beneficial alleles in various crops such as rice, tomato, wheat and barley. For the development of an AB population, a controlled crossing scheme is used and this controlled crossing along with the selection (both natural and artificial) of agronomically-adapted alleles during the development of AB population may lead to unbalanced allele frequencies in the population. However, it is commonly believed that interval mapping mapping of traits in experimental crosses such as AB populations are immune to the deviations from the expected frequencies under Mendelian segregation. Using two AB populations and simulated data sets as examples, we describe the severity of the problem caused by unbalanced allele frequencies in quantitative trait loci (QTL) mapping and demonstrate how it can be corrected using the linear mixed model having a polygenic effect with the covariance structure (genomic relationship matrix) calculated from molecular markers.

Identification of Swarna x O. nivara (RPBio4918) advanced backcross lines performing well under acidic soil conditions

Aim: To evaluate a set of ABLs (Advanced Backcross Lines) to identify lines perfoming well under acidic soil and iron toxicity hydroponics conditions. Methodology: A total of 194 ABLs were randomly used in lowland field randomly following augmented experimental design. Selected lines were screened in hydroponics condition using Yoshida’s solution for iron toxicity tolerance. Results: Under field conditions, several deficiencies and toxicities often co-exist, and it becomes difficult to partition the effect of different stresses on the genotypes. Therefore, screening genotypes in artificial hydroponics conditions allows us to dissect the response of a genotype to one particular nutrient toxicity or deficiency. Based on different traits superior, average and inferior performing lines were selected from field condition. Hydroponic experiment was conducted using Yoshida’s solution for iron toxicity screening, different superior and inferior lines were identified based on the parameters like root growth, root and shoot biomass. Four lines K 408, K 455, S 304, S 203 were identified that performed well in both field and Fe toxic hydroponic conditions. Interpretation: The information generated would help to identify suitable parents for breeding program under acidic soils, and the phenotypic data on ABLs may serve as a base for future mapping of loci responsible for yield under acidic soils and iron toxic conditions. Key words: Acidic soil, Advanced backcross lines, Hydroponic condition, Iron toxicity, Seedling stage screening