Genetic loci responding to two cycles of divergent selection for grain yield under drought stress in a rice breeding population

Molecular marker loci responding to selection under drought stress were monitored in a rice breeding population obtained by crossing a tolerant parent (Apo) to a susceptible parent (IR64). The 40 highest-yielding lines under stress and non-stress conditions obtained after two cycles of divergent selection under drought stress and non-stress conditions, respectively were genotyped using 72 polymorphic and widely distributed SSR markers. Ten loci (RM572, RM6703, RM71, RM3387, RM5686, RM520, RM510, RM256, RM269 and RM511) showing highly significant allele frequency differences between the two sets were identified. Favorable alleles at eight of these loci came from the tolerant parent, and at two (RM3387 and RM510) from the susceptible parent (IR64). Effects of these loci on grain yield were tested in five independent experiments covering a range in soil moisture levels. Results showed that at six loci (RM572, RM6703, RM520, RM256, RM269, and RM511), Apo alleles had highly significant effects on grain yield in at least three of the four stress trials but only two of these loci (RM572 and RM511) also affected grain yield under non-stress conditions. In all these cases, the effects of loci generally increased with stress level. Apo alleles at these loci seem to enhance yield under stress mainly by increasing harvest index and reducing flowering delay. Large-effect quantitative trait loci (QTLs) affecting grain yield under upland drought stress have already been found previously in other populations near RM6703, RM520, and RM511. Thus, these regions appear to be important in explaining genetic variation for upland drought tolerance in rice.     

Rph23: A new designated additive adult plant resistance gene to leaf rust in barley on chromosome 7H

We report on a new adult plant resistance (APR) gene Rph23 conferring resistance to leaf rust in barley. The gene was identified and characterized from a doubled haploid population derived from an intercross between the Australian barley varieties Yerong (Y) and Franklin (F). Genetic analysis of adult plant field leaf rust scores of the Y/F population collected over three successive years indicated involvement of two highly additive genes controlling APR, one of which was named Rph23. The gene was mapped to chromosome 7HS positioned at a genetic distance 36.6 cM. Rph23 is closely linked to marker Ebmac0603, which is flanked by markers bPb‐8660 and bPb‐9601 with linkage distances of 0.8 and 5.1 cM, respectively. A PCR‐based marker was optimized for marker‐assisted selection of Rph23, and on the basis of this marker, the gene was postulated as being common in Australian and global barley germplasm. Pedigree and molecular marker analyses indicated that the six‐rowed black Russian landrace ‘LV‐Taganrog’ is the likely origin of Rph23.     

Relationship of Carbon Isotope Discrimination to Water Use Efficiency and Productivity of Barley Under Field and Greenhouse Conditions

This study was conducted to evaluate the application of carbon isotope discrimination (CID) as a selection criterion for improving water use efficiency (WUE) and productivity of barley (Hordeum vulgare L.) under field and drought‐stress conditions in a greenhouse. A total of 54 genotypes were screened for variability in CID under field conditions, while 23 genotypes were evaluated under water‐deficit conditions in the greenhouse. A survey of leaf CID of 54 genotypes at two field locations showed more than 2.14‰ difference between extreme genotypes. Significant (P ≤ 0.05) genotypic variation was found in WUE and CID that had a negative strong correlation. There was a negative correlation between leaf CID and aerial biomass in the greenhouse and among six‐row genotypes in the field. Correlations between leaf CID across field locations and across irrigation regimes in the greenhouse were significant (experiment 1, r = 0.79 and 0.94 for six‐ and two‐row genotypes), suggesting stability of the CID trait across different environments. Overall, these results indicate the potential of leaf CID as a reliable method for selecting for high WUE and productivity in barley breeding programmes in the Canadian prairies. Further work is currently underway to determine heritability/genetics of leaf CID and application of molecular marker‐assisted selection for the traits in barley breeding programmes.     

Screening oat germplasm for better adaptation to cold stress in the Southern Great Plains of the United States

Oat (Avena sativa L.) is one of the most important forage crops in the Southern Great Plains of the United States. However, it is more sensitive to cold stress than other small grains. In this study, diverse oat germplasm was evaluated for winter survival across multiple years and locations in the region. Field screening started with an observation trial of 1,861 diverse genotypes in the 2012–2013 season and was followed by four seasons of replicated trials from 2013 to 2017. Selection of good winter survivors was started in 2014–2015 season. All trials were laid out in randomized complete blocks with replications of two in 2013–2014 and 2014–2015, four in 2015–2016, and three in 2016–2017. Winter survival was scored in a 1‐to‐9 scale. Data were analysed for each year and location separately. Additive main effects and multiplicative interaction (AMMI) analysis were carried out on combined data of 35 genotypes that were commonly grown in each year and location. Highly significant (p < 0.001) variations were observed among genotypes, environments and genotype‐by‐environment interaction (GEI). The first three interaction principal components (IPCs) were highly significant (p < 0.001), explaining 96% of GEI. Broad sense heritability ranged from 46% to 93%, while heritability for all environments combined was relatively low (24.6%). At the end of the two cycles (2014/2015‐to‐2016/2017) of selection, mean winter survival was improved by more than 38% per cycle compared with the base population mean. Genotypes CIav 4390, CIav 6909 and CIav 7618 showed significantly higher winter survival than the standard checks Okay and Dallas. Genotypes CIav 4390 showed 20% and 35% improvement over the standard checks Okay and Dallas, respectively. Winter survival improvement in oat will remain a difficult task because of high GEI and low heritability. The identified superior genotypes will be used as crossing parents to transfer cold tolerance genes to other elite lines.     

Genetic diversity among populations and breeding lines from recurrent selection in Brassica napus as revealed by RAPD markers

Recurrent selection facilitated by dominant male sterility has been conducted to broaden the genetic basis for cultivar development in Brassica napus. This study aimed to evaluate the genetic variation in four base populations (C0‐C3) and breeding lines from two of the populations produced during recurrent selection by random amplified polymorphic DNA (Rapd) markers. Genetic variation in four populations declined gradually with the advance of selection cycles as measured by expected genetic heterozygosity (from 0.2058 in C0 to 0.1536 in C3) but the decline was not statistically significant. When compared with the average genetic distances for 21 germplasm collections with wide geographical and genetic origins (0.4712) and seven breeding lines from pedigree selection (0.2059), seven breeding lines selected from the C1 population and 11 from the C3 population had a larger average genetic distance (0.5339 and 0.5486, respectively). Clustering analysis indicated that the lines from recurrent selection had a much lower genetic similarity than lines from pedigree selection. Our results suggest that base populations derived from recurrent selection could provide a wider genetic variation for selection of breeding lines with more broad genetic bases.     

Resistance to Fusarium crown rot in wheat and barley: a review

Fusarium crown rot (FCR) is becoming a major disease in many parts of the cereal‐growing regions worldwide. Significant QTL conferring FCR resistance have been reported on 13 of the 21 possible hexaploid wheat chromosomes in wheat and on three of the seven chromosomes in barley. Available results show that host resistance to FCR is not pathogen species‐specific, that resistance QTL have strong additive effect and that both plant height and growth rate affect FCR severity. Further, different loci seem to be responsible for resistances to FCR and Fusarium head blight although both diseases can be caused by the same Fusarium pathogens. Although marker‐assisted selection for FCR resistance has been initiated, the available markers are all derived from QTL mapping, which provides only limited resolution. Further work has to be conducted in developing diagnostic markers before significant progress can be made in deploying marker‐assisted selection as a routine tool to accelerate and improve FCR in breeding programmes.     

An extension of the Smith model for quantitative genetic analysis of selection response under recurrent selection

Selection and random genetic drift are the main forces affecting selection response in recurrent selection (RS) programmes. The correct assessment of both forces allows a better comparison of the efficiency of different RS schemes. The objective of this study was to extend the population diallel analysis proposed by Hammond and Gardner in 1974 and the model proposed by Smith in 1979 with full consideration of inbreeding depression due to random genetic drift. The effect of random genetic drift is expected to be large, particularly in studies with many selection cycles and/or high rates of inbreeding. Therefore, the extension of the population diallel allows a better assessment of the selection response in RS programmes.     

Molecular diversity and association mapping of quantitative traits in Tibetan wild and worldwide originated barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.) germplasm

Molecular diversity of 40 accessions of Tibetan wild barley (TB), 10 Syrian (SY), 72 North American (NA), 36 European (EU), 9 South American (SA) and 8 Australian (AU) varieties were characterized using multiple microsatellite loci. The 42 SSR primers amplified 278 alleles across the 175 barley accessions tested in the present study. The average gene diversity for the whole sample was 0.3387 whereas the mean value for the each population was as follows: TB = 0.3286, SY = 0.2474, EU = 0.299, AU = 0.2867, NA = 0.3138, SA = 0.2536. Clustering analysis based on Nei’s original genetic distance showed that the EU and NA barley populations were grouped together. The TB population was well separated from the other 5 barley populations. Associations between microsatellite markers and 14 quantitative traits were also investigated. Significant associations were found for 18 microsatellite marker loci. The number of marker loci associated with each trait ranged from one (stem diameter, filled grains per plant, grain weight per plant, length of main spike and awn length) to seven (plant height). The percentage of the total variation explained by each marker ranged from 4.59% (HVM2 associated with plant height) to 17.48% (Bmac90 associated with density of main spike). This study provides candidate markers for further QTL mapping of these traits and for marker-assisted selection.     

Outcrossing Rates in Autumn and Spring-Sown Barley

Natural outcrossing is a potential cause of the admixtures which are often observed, especially in winter barley. Outcrossing was studied in yield trials with hap laid -derived homozygous offspring, lines from tour crosses between winter and spring barley varieties. Outcrosses were recognised by heterozygosity in storage protein loci Hor1 and Hor2 as revealed by electrophoresis. Outcrossing, was, on average, about 5% in lines sown in the autumn and less than 0.5% after spring sowing. Autumn-sown lines from one of the four crosses studied had about 10% outcrosses.     

The potential of genomic‐assisted breeding to improve Fusarium head blight resistance in winter durum wheat

Durum wheat is the most important tetraploid wheat mainly used for semolina and pasta production, but is notorious for its high susceptibility to Fusarium head blight (FHB). Our objectives were to identify and characterize quantitative trait loci (QTL) in winter durum and to evaluate the potential of genomic approaches for the improvement of FHB resistance. Here, we employed an international panel of 170 winter and 14 spring durum lines, phenotyped for Fusarium culmorum resistance at five environments. Heading date, plant height and mean FHB severity showed significant genotypic variation with high heritabilities and FHB resistance was negatively correlated with both heading date and plant height. The dwarfing gene Rht‐B1 significantly affected FHB resistance and the genome‐wide association scan identified eight additional QTL affecting FHB resistance, explaining between 1% and 14% of the genotypic variation. A genome‐wide prediction approach yielded only a slightly improved predictive ability compared to marker‐assisted selection based on the four strongest QTL. In conclusion, FHB resistance in durum wheat is a highly quantitative trait and in breeding programmes may best be tackled by classical high‐throughput recurrent phenotypic selection that can be assisted by genomic prediction if marker profiles are available.     

Comparison of selection methods on ‘Pigarro’, a Portuguese improved maize population with fasciation expression

In 1984, Pêgo started, with the CIMMYT support, an on-farm participatory maize breeding (PMB) project at the Portuguese Sousa Valley region (VASO). VASO was intended to answer the needs of small farmers (e.g., yield, bread making quality, ability for polycropping systems). During 20 years of PMB at VASO, mass (MS) and S2 recurrent selection (S2RS) were applied on the maize landrace ‘Pigarro’. Morphological (e.g., ear length and fasciation level) and yield evaluations were conducted in Portugal (2–3 locations in 2 years) and in USA (4 locations in one year) using samples from original population, six MS cycles and three S2RS cycles. North American Populations (BS21, BS22, TEPR-EC6) were also included as checks. ANOVA comparisons and regression analyses on the rate of direct response to selection were performed. Response to MS for Iowa showed significant decrease in stalk lodging, while in Portugal ear length significantly decreased, whereas ear diameter, kernel-row number, and fasciation level significantly increased. Selection also significantly increased days-to-silk and anthesis in Portugal. Response to S2RS in Portugal significantly increased days-to-silk, uniformity, and cob/ear weight ratio. These results showed that the methods used by farmer and breeder were not effective for significant yield increase, but the ear size increased significantly for MS and showed a positive tendency for S2RS. Adaptation to farmer needs was maintained for the last cycles of selection.     

Evaluation of floral characteristics of barley in the semi-arid climate of north Syria

Previous studies have revealed that, in areas affected by severe drought, yielding ability and stability of barley (Hordeum vulgare L.) could be improved by increasing the level of heterozygosity. One possible approach to increase the heterozygosity level is to improve the outcrossing rate. In view of that, the genetic variability and phenotypic correlation coefficients involving four floral traits related to outcrossing behaviour were investigated in 274 drought adapted barley lines from the International Center for Agricultural Research in the Dry Areas (ICARDA's) current breeding programme. A significant quantitative variation existed in anther length and width, stigma length, and anther extrusion, which indicate that selection for these traits may be effective. Anther extrusion showed weak but highly significant positive correlations with anther and stigma length. Somewhat higher positive correlations were found between anther and stigma length. The results indicate that selection for high anther extrusion and longer anthers and stigmata may increase outcrossing in cultivated barley and consequently improve yielding ability through enhanced heterozygosity.     

Genetic mapping of the barley lodging resistance locus Erectoides‐k

The barley (Hordeum vulgare L.) mutant erectoides‐k.32 (ert‐k.32) was isolated in 1947 from an X‐ray‐mutant population of cultivar ‘Bonus’. The mutant was released as a cultivar in 1958 with the name ‘Pallas’ – one of the first cereal crop cultivars developed from induced mutants. ‘Pallas’ is a semi‐dwarf barley cultivar known for its culm stability and resistance to lodging. In total, eight allelic ert‐k mutants are known that show different phenotypic strength concerning culm length and spike architecture. They represent alternatives to the widely used, but pleiotropic ‘Green Revolution’ alleles of the Sdw1 (semidwarf1/denso) and Uzu1 (semi‐brachytic1) genes in breeding of robust elite barley cultivars. In the present study, we locate Ert‐k to a 15.7‐cM region in the centromeric region of chromosome 6H. Although the interval is estimated to contain approximately 700 genes, the work provides a solid foundation for the identification of the underlying mutations causing the ert‐k lodging‐resistant phenotype. In addition, the linked markers could be used to follow the ert‐k mutant genotype in marker‐assisted selection of new lodging‐resistant barley cultivars.     

Genome‐wide association studies in elite varieties of German winter barley using single‐marker and haplotype‐based methods

Genome‐wide association studies (GWAS) became a widely used method to map qualitative and quantitative traits in plants. We compared existing single‐marker and haplotype‐based methods for GWAS with a focus on barley. Based on German winter barley cultivars, four different single‐marker and haplotype‐based methods were tested for their power to detect significant associations in a large genome with a limited number of markers. We identified significant associations for yield and quality‐related traits using the iSelect array with 3886 mapped single nucleotide polymorphism (SNP) markers in a structured population consisting of 109 genotypes. Genome simulations with different numbers of genotypes, marker densities and marker effects were used to compare different GWAS methods. Results of simulations revealed a higher power in detecting significant associations for haplotype‐ than for single‐marker approaches, but showed a higher false discovery rate for SNP detection, due to lack of correction for population structure. Our simulations revealed that a population size of about 500 individuals is required to detect QTLs explaining a small trait variance (<10%).     

Genetic mapping of the barley Rrs14 scald resistance gene with RFLP, isozyme and seed storage protein markers

The scald susceptible barley cultivar ‘Clipper’ and a third‐backcross (BC₃) line homozygous for the Rrs14 scald resistance gene that originally came from Hordeum vulgare ssp. spontaneum were grown in replicated field trials. The level of resistance that Rrs14 confers against field populations of the pathogen Rhynchosporium secalis, the causal agent of scald disease, was evaluated. The Rrs14 BC₃ line exhibited 80% and 88% less leaf damage than ‘Clipper’ in 1995 and 1996, respectively. Given this effectiveness of Rrs14, research was undertaken to identify a linked marker locus suitable for indirect selection of Rrs14. Based on linkage to a set of previously mapped loci, Rrs14 was positioned to barley chromosome 1H between the seed storage protein (hordein) loci Hor1 and Hor2, approximately 1.8 cM from the latter locus. The Hor2 locus is thus an ideal codominant molecular marker for Rrs14. The tight linkage between Rrs14 and Hor2 and the availability of alternative biochemical and molecular techniques for scoring Hor2 genotypes, permits simple indirect selection of Rrs14 in barley scald resistance breeding programmes.     

Divergent Selection for Heading Date in Barley

Divergent selection for heading time was performed in two F₂ barley population. Five populations were obtained for each cross: F₅ SSD (unselected control), 3E and 3L (from three cycles of selection for earliness or lateness), 2E1L and ZL1E (from two cycles of direct and one of reverse selection). These populations, together with corresponding parents and F₂ generations, were evaluated over two years. The response to selection was 5.6 and 6.5 days inane direction (earlier heading) and 7.7 and 6.7 clays in the other direction (later heading) in the two crosses, respectively. 3E and 3L populations were highly transgressive as compared to their parents. A sizeable amount of genetic variability was still present after two cycles of selection. Heading was probably controlled by a polygenic system with prevailing additive effects and alleles for earliness and earliness somewhat equally distributed in the parents. Selection fur heading time led to significant changes in plant height, yield and kernel weight. Early progenies were higher yielding than lace ones.     

Mass selection of wheat for grain filling without transient photosynthesis

Summary Post-anthesis chemical desiccation of wheat (Triticum aestivum L.) plants in the field eliminates transtent photosynthesis by killing all green tissues, thus revealing the plant's capacity for grain filling from stored stem reserves, as the case is for post-anthesis stress such as drought or leaf diseases. This study was conducted to investigate whether mass selection for large kernels under chemical desiccation would lead to the improve ment of grain filling in the absence of transient photosynthesis.Six crosses of common spring wheat were subjected to three cycles of mass selection from F₂ through F₁ when selection was performed for large kernels by sieving grains from plants that were erther chemically desiccated after anthesis, or not (controls). The resulting 36 bulks (six crosses by three selection cycles by two selection environments) were compared with their respective F₂ base populations, when tested with and without chemical desiccation.Selection for large kernels under potential conditions (without chemical desiccation) did not improve kernel weight under potnetial conditions, evidently because these materials were lacking in genetic variation for kernel weight under potential conditions. In four of the crosses, 3rd cycle selection for large kernels under potential conditions decreased kernel weight under chemical desiccation. On the other hand, selection for large kernels under chemical desiccation was effective in improving kernel weight and test weight under chemical desiccation, depending on the cross and the selection cycle, with no genetic shift in mean days to heading or mean plant height. Selection for large kernels under chemical desiccation was also effective in some cases in increasing kernel weight under potential conditions. The results are interpreted to show that selection under potential conditions and under chemical desiccation operate on two different sources for grain filling, namely transient photosynthesis and stem reserve utilization, respectively. In order to expose genetic variability for stem reserve utilization to selection pressure, transient photosynthesis must be eliminated, as done by chemical desiccation in this study.     

Marker-assisted backcross introgression of the Yd2 gene conferring resistance to barley yellow dwarf virus in barley

YLM, a codaominant polymerase chain reaction (PCR) marker linked to Yd2, could substantially improve the precision and efficiency of barley yellow dwarf virus (BYDV) resistance breeding. The aim of this study was to assess the effectiveness of YLM in a marker‐assisted introgression programme and to quantify associations between the presence of Yd2 and other agronomic and quality traits. The Yd2 gene was introgressed into a BYDV‐susceptible background through two cycles of marker‐assisted backcrossing. BC₂ F₂‐derived lines, either carrying or not carrying the YLM allele associated with resistance, were compared in the presence and absence of BYDV. The YLM marker was shown to be effective in the introgression of Yd2. Lines carrying the YLM allele associated with resistance produced significantly fewer leaf symptoms and showed a reduction in yield loss when infected with BYDV. There were no deleterious effects associated with the introgression of Yd2 on grain yield, grain size or malting quality. The implications of marker‐assisted selection for Yd2 on barley improvement are discussed.     

Changes in allele frequencies in landraces, old and modern barley cultivars of marker loci close to QTL for grain yield under high and low input conditions

Changes in alleles frequencies of marker loci linked to yield quantitative trait loci (QTL) were studied in 188 barley entries (landraces, old and modern cultivars) grown in six trials representing low and high yielding conditions in Spain (2004) and Syria (2004, 2005). A genome wise association analysis was performed per trial, using 811 DArT^® markers of known map position. At the first stage of analysis, spatially adjusted genotypic means were created per trial by fitting mixed models. At the second stage, single QTL models were fitted with correction for population substructure, using regression models. Finally, multiple QTL models were constructed by backward selection from a regression model containing all significant markers from the single QTL analyses. In addition to the association analyses per trial, genotype by environment interaction was investigated across the six trials. Landraces seemed best adapted to low yielding environments, while old and modern entries adapted better to high yielding environments. The number of QTL and the magnitude of their effects were comparable for low and high input conditions. However, none of the QTL were found within a given bin at any chromosome in more than two of the six trials. Changes in allele frequencies of marker loci close to QTL for grain yield in landraces, old and modern barley cultivars could be attributed to selection exercised in breeding, suggesting that modern breeding may have increased frequencies of marker alleles close to QTL that favour production particularly under high yield potential environments. Moreover, these results also indicate that there may be scope for improving yield under low input systems, as breeding so far has hardly changed allele frequencies at marker loci close to QTL for low yielding conditions.