Showing papers on "Plant breeding published in 2017"

Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits

Abstract: Upland cotton (Gossypium hirsutum) is the most important natural fiber crop in the world. The overall genetic diversity among cultivated species of cotton and the genetic changes that occurred during their improvement are poorly understood. Here we report a comprehensive genomic assessment of modern improved upland cotton based on the genome-wide resequencing of 318 landraces and modern improved cultivars or lines. We detected more associated loci for lint yield than for fiber quality, which suggests that lint yield has stronger selection signatures than other traits. We found that two ethylene-pathway-related genes were associated with increased lint yield in improved cultivars. We evaluated the population frequency of each elite allele in historically released cultivar groups and found that 54.8% of the elite genome-wide association study (GWAS) alleles detected were transferred from three founder landraces: Deltapine 15, Stoneville 2B and Uganda Mian. Our results provide a genomic basis for improving cotton cultivars and for further evolutionary analysis of polyploid crops.

High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth

Abstract: With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize (Zea mays) recombinant inbred line population (n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction.

Phenotyping of field-grown wheat in the UK highlights contribution of light response of photosynthesis and flag leaf longevity to grain yield.

Abstract: Improving photosynthesis is a major target for increasing crop yields and ensuring food security. Phenotyping of photosynthesis in the field is critical to understand the limits to crop performance in agricultural settings. Yet, detailed phenotyping of photosynthetic traits is relatively scarce in field-grown wheat, with previous studies focusing on narrow germplasm selections. Flag leaf photosynthetic traits, crop development, and yield traits were compared in 64 field-grown wheat cultivars in the UK. Pre-anthesis and post-anthesis photosynthetic traits correlated significantly and positively with grain yield and harvest index (HI). These traits included net CO2 assimilation measured at ambient CO2 concentrations and a range of photosynthetic photon flux densities, and traits associated with the light response of photosynthesis. In most cultivars, photosynthesis decreased post-anthesis compared with pre-anthesis, and this was associated with decreased Rubisco activity and abundance. Heritability of photosynthetic traits suggests that phenotypic variation can be used to inform breeding programmes. Specific cultivars were identified with traits relevant to breeding for increased crop yields in the UK: pre-anthesis photosynthesis, post-anthesis photosynthesis, light response of photosynthesis, and Rubisco amounts. The results indicate that flag leaf longevity and operating photosynthetic activity in the canopy can be further exploited to maximize grain filling in UK bread wheat.

Gains in Maize Genetic Improvement in Eastern and Southern Africa: I. CIMMYT Hybrid Breeding Pipeline

Abstract: Monitoring of genetic gain in crop genetic improvement programs is necessary to measure the efficiency of the program. periodic measurement of genetic gain also allows the efficiency of new technologies incorporated into a program to be quantified. Genetic gain within the International Maize and Wheat Improvement Centre (CIMMYT) breeding program for eastern and southern Africa were estimated using time series of maize (Zea mays L.) hybrids. A total of 67 of the best-performing hybrids from regional trials from 2000 to 2010 were selected to form an era panel and evaluated in 32 trials in eight locations across six countries in eastern and southern Africa. Treatments included optimal management, managed and random drought stress, low-nitrogen (N) stress and maize streak virus (MSV) infestation. Genetic gain was estimated as the slope of the regression of grain yield on the year of hybrid release. Genetic gain under optimal conditions, managed drought, random drought, low N, and MSV were estimated to have increased by 109.4, 32.5, 22.7, 20.9 and 141.3 kg ha−1 yr−1, respectively. These results are comparable with genetic gain in maize yields in other regions of the world. New technologies to further increase the rate of genetic gain in maize breeding for eastern and southern Africa are also discussed. J.E. Cairns, B. Masuka, J. Macrobert, C. Magorokosho, A. Tarekegne, and M. Zaman-Allah, International Maize and Wheat Improvement Centre (CIMMYT), PO Box MP163, Harare, Zimbabwe; G. Alvarado, J. Crossa, M. Bänziger, and K.V. Pixley, CIMMYT, Km. 35 Carr. Mexico-Veracruz, Texcoco, Edo de Mexico, DF, Mexico; G.N. Atlin, Bill & Melinda Gates Foundation, PO Box 23350, Seattle, WA 98102; B.M. Prasanna, B. Das, M. Olsen, and D. Makumbi, CIMMYT, United Nations Avenue, Gigiri PO Box 1041, Village Market 00621, Nairobi, Kenya; M. Labushchangne and A. von Biljong, Dep. of Plant Sciences, Univ. of Free State, South Africa; B.S. Vivek, CIMMYT, Patancheru 502 324, India. Received 16 May 2016. Accepted 8 Sept. 2016. *Corresponding author ( j.cairns@cgiar.org). Assigned to Associate Editor Jode Edwards. Abbreviations: ASI, anthesis–silking interval; CIMMYT, International Maize and Wheat Improvement Center; DH, doubled haploid; ESA, eastern and southern Africa; GCA, general combining ability; MSV, maize streak virus; OPV, open-pollinated variety; QTLs, quantitative trait loci; SNP, single-nucleotide polymorphism; SSA, sub-Saharan Africa. Published in Crop Sci. 57:168–179 (2017). doi: 10.2135/cropsci2016.05.0343 © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA This is an open access article distributed under the CC BY license (https:// creativecommons.org/licenses/by/4.0/). Published January 19, 2017

A systematic review of rye (Secale cereale L.) as a source of resistance to pathogens and pests in wheat (Triticum aestivum L.).

Abstract: Wheat is globally one of the most important crops With the current human population growth rate, there is an increasing need to raise wheat productivity by means of plant breeding, along with development of more efficient and sustainable agricultural systems Damage by pathogens and pests, in combination with adverse climate effects, need to be counteracted by incorporating new germplasm that makes wheat more resistant/tolerant to such stress factors Rye has been used as a source for improved resistance to pathogens and pests in wheat during more than 50 years With new devastating stem and yellow rust pathotypes invading wheat at large acreage globally, along with new biotypes of pest insects, there is renewed interest in using rye as a source of resistance Currently the proportion of wheat cultivars with rye chromatin varies between countries, with examples of up to 34% There is mainly one rye source, Petkus, that has been widely exploited and that has contributed considerably to raise yields and increase disease resistance in wheat Successively, the multiple disease resistances conferred by this source has been overcome by new pathotypes of leaf rust, yellow rust, stem rust and powdery mildew However, there are several other rye sources reported to make wheat more resistant to various biotic constraints when their rye chromatin has been transferred to wheat There is also development of knowledge on how to produce new rye translocation, substitution and addition lines Here we compile information that may facilitate decision making for wheat breeders aiming to transfer resistance to biotic constraints from rye to elite wheat germplasm

Effect of colchicine-induced polyploidy on morphological characteristics and essential oil composition of ajowan ( Trachyspermum ammi L.)

Abstract: Polyploidy is an amazing evolutionary event that can be used in plant breeding to improve plant material The present study was conducted to assess the effect of in vitro-induced polyploidy on different properties of Ajowan medicinal plant Five different concentrations of colchicine, including 0025, 005, 01, 02, and 05% (w/v), were applied to germinating seeds of ajowan in six different durations of exposure, including 6, 12, 24, 36, and 48 h Chromosome counting showed successful duplication of chromosome number in tetraploid plants (2n = 4x = 36) in contrast with intact diploid plants (2n = 2x = 18) DNA content duplication in induced tetraploid plants was proved through flow cytometry analysis The highest tetraploidy induction was achieved by applying 005% (w/v) colchicine for 24 h with 1153% efficiency The tetraploid plants achieved were larger than their diploid intact plants for plant height, leaf length, stem diameter, inflorescence length, peduncle length, and seed length characteristics The length and width of stomata were increased in induced tetraploid plants, whereas stomata density was decreased, in contrast with initial diploid plants Gas chromatography mass spectrometry (GC/MS) analysis showed significant increases in thymol content in essential oil of tetraploid plants (692%) in contrast with those of diploid plants (4967%)

A new method for evaluating the drought tolerance of upland rice cultivars

Abstract: Worldwide, approximately 27 million ha of rice are grown in upland rather than paddy fields, and is subject to drought stress. To counter this stress, it is desirable to breed new rice cultivars with improved drought tolerance. For breeding purposes, especially for breeding upland rice, it is desirable to develop a simple and accurate method to evaluate rice drought tolerance. We describe a new method that can be used to evaluate efficiently the drought tolerance degree (DTD) of upland rice cultivars, and call it the DTD method. DTD is defined as the mean of the ratios of green leaf length to total leaf length of the top three leaves in every rice seedling after drought treatment, and thus takes values from zero to one. To test whether the DTD method works effectively to evaluate drought tolerance of upland rice cultivars, we determined the DTD values of 13 upland rice cultivars showing varying degrees of drought tolerance in drought-tolerance trials. The idr1-1 mutant, which displayed the strongest drought tolerance of the 13 cultivars as identified by drought-tolerance trials under severe drought stress, had the highest DTD value and 297-28, displaying the weakest drought tolerance, had the lowest DTD value. Further analyses of water potential, survival rate, panicles per plant, spikelets per panicle, seed setting rate, yield per plant, and contents of proline, chlorophyll, and malondialdehyde (MDA) indicated that DTD values are in general correlated with the values of these traits, making this new method useful for assessing the drought tolerance of upland rice cultivars. These results show that the DTD method is a simple, direct and relatively accurate evaluation method for drought-tolerance breeding of upland rice.

Bringing New Plant Varieties to Market: Plant Breeding and Selection Practices Advance Beneficial Characteristics while Minimizing Unintended Changes

Abstract: Commercial-scale plant breeding is a complex process in which new crop varieties are continuously being developed to improve yield and agronomic performance over current varieties. A wide array of naturally occurring genetic changes are sources of new characteristics available to plant breeders. During conventional plant breeding, genetic material is exchanged that has the potential to beneficially or adversely affect plant characteristics. For this reason, commercial-scale breeders have implemented extensive plant selection practices to identify the top-performing candidates with the desired characteristics while minimizing the advancement of unintended changes. Selection practices in maize (Zea mays L.) breeding involve phenotypic assessments of thousands of candidate lines throughout hundreds of different environmental conditions over many years. Desirable characteristics can also be introduced through genetic modification. For genetically modified (GM) crops, molecular analysis is used to select transformed plants with a single copy of an intact DNA insert and without disruption of endogenous genes. All the while, GM crops go through the same extensive phenotypic characterization as conventionally bred crops. Data from both conventional and GM maize breeding programs are presented to show the similarities between these two processes.

Harnessing the hidden genetic diversity for improving multiple abiotic stress tolerance in rice (Oryza sativa L.).

Abstract: To develop superior rice varieties with improved yield in most rainfed areas of Asia/Africa, we started an introgression-breeding program for simultaneously improving yield and tolerances of multiple abiotic stresses. Using eight BC1 populations derived from a widely adaptable recipient and eight donors plus three rounds of phenotypic selection, we developed 496 introgression lines (ILs) with significantly higher yield under drought, salt and/or non-stress conditions in 5 years. Six new varieties were released in the Philippines and Pakistan and many more are being evaluated in multi-location yield trials for releasing in several countries. Marker-facilitated genetic characterization revealed three interesting aspects of the breeding procedure: (1) the donor introgression pattern in specific BC populations was characteristic; (2) introgression frequency in different genomic regions varied considerably, resulting primarily from strong selection for the target traits; and (3) significantly lower heterozygosity was observed in BC progenies selected for drought and salinity tolerance. Applying strong phenotypic selection under abiotic stresses in early segregating generations has major advantages for not only improving multiple abiotic stress tolerance but also achieving quicker homozygosity in early generations. This breeding procedure can be easily adopted by small breeding programs in developing countries to develop high-yielding varieties tolerant of abiotic stresses. The large set of trait-specific ILs can be used for genetic mapping of genes/QTL that affect target and non-target traits and for efficient varietal development by designed QTL pyramiding and genomics-based recurrent selection in our Green Super Rice breeding technology.

Genetic Architecture of Anther Extrusion in Spring and Winter Wheat

Abstract: Hybrid wheat breeding is gaining prominence worldwide because it ensures higher and more static yield than conventionally bred varieties The cleistogamous floral architecture of wheat (Triticum aestivum L) impedes anthers inside the floret, making it largely an inbreeder For hybrid seed production, high anther extrusion is needed to promote cross pollination and to ensure a high level of pollen availability for the seed plant This study, therefore, aimed at the genetic dissection of anther extrusion (AE) in panels of spring (SP) and winter wheat (WP) accessions by genome wide association studies (GWAS) We performed GWAS to identify the SNP markers potentially linked with AE in each panel separately Phenotypic data were collected for three years for each panel The average levels of Pearson’s correlation (r) among all years and their best linear unbiased estimates (BLUEs) within both panels were high (r (SP) = 075, P 30) marker trait associations (MTAs) were detected in both panels (SP = 11; WP = 12) Anther extrusion behaved as a complex trait with significant markers having either favourable or unfavourable additive effects and imparting minor to moderate levels of phenotypic variance (R2 (SP) = 975 – 1424%; R2 (WP) = 944 – 1698%) All mapped significant markers as well as the markers within their significant linkage disequilibrium (r2 ≥03) regions were blasted against wheat genome assembly (IWGSC1+popseq) to find the corresponding genes and their high confidence descriptions were retrieved These genes and their orthologues in Hordeum vulgare, Brachypodium distachyon, Oryza sativa and Sorghum bicolor revealed syntenic genomic regions potentially involved in flowering-related traits Moreover, the expression data of these genes suggested potential candidates for AE Our results suggest that the use of significant markers can help to introduce AE in high yielding varieties to increase cross fertilization rates and improve hybrid-seed production in wheat

Comparative Analysis of Root Traits and the Associated QTLs for Maize Seedlings Grown in Paper Roll, Hydroponics and Vermiculite Culture System.

Abstract: Root system architecture (RSA) has an important role in nitrogen (N) and phosphorus (N) acquisition, but RSA is seldom considered as a selection criterion to improve nutrient uptake efficiency in crop breeding as roots are greatly influenced by uncontrolled environment factors under field conditions. Therefore, it is necessary to develop fast selection methods for evaluating root traits of young seedlings in the lab which can then be related to high nutrient efficiency of adult plants in the field. Here, a maize recombination inbred lines (RILs) population was used to compare the genetic relationship between RSA and nitrogen and phosphorous efficiency traits. The phenotypes of eight RSA-related traits were evaluated in young seedlings in three different growth systems (i.e. paper roll, hydroponics and vermiculite), and then subjected to correlation analysis with N efficiency and P efficiency related traits measured under field conditions. Quantitative trait loci (QTL) of RSA were determined and QTL co-localizations across different growth systems were further analyzed. Phenotypic associations were observed for most of RSA traits among all three culture systems. Correlations of RSA-related traits in hydroponics and vermiculite with N (NupE) uptake efficiency (r = 0.17-0.31) and P (PupE) uptake efficiency (r = 0.22-0.34) were significant but weak, and not in paper roll. A total of 14 QTLs for RSA were identified in paper rolls, 18 in hydroponics, and 14 in vermiculite. Co-localization of QTLs for RSA traits were identified in six chromosome regions of bin 1.04/1.05, 1.06, 2.04/2.05, 3.04, 4.05 and 5.04/5.05. These results suggest the difficulty that uses the phenotypes from one growth system to predict those in another growth system. Additionally, RSA traits at seedling stage with hydroponics and vermiculite systems is better than paper roll system to be used as an important index to accelerate the selection of high N and P efficiency genotypes for maize breeding programs.

Genetic map of mango: a tool for mango breeding

Abstract: Mango (Mangifera indica) is an economically and nutritionally important tropical/subtropical tree fruit crop. Most of the current commercial cultivars are selections rather than the products of breeding programs. To improve the efficiency of mango breeding, molecular markers have been used to create a consensus genetic map that identifies all 20 linkage groups in seven mapping populations. Polyembryony is an important mango trait, used for clonal propagation of cultivars and rootstocks. In polyembryonic mango cultivars, in addition to a zygotic embryo, several apomictic embryos develop from maternal tissue surrounding the fertilized egg cell. This trait has been associated with linkage group 8 in our consensus genetic map and has been validated in two of the seven mapping populations. In addition, we have observed a significant association between trait and single nucleotide polymorphism (SNP) markers for the vegetative trait of branch habit and the fruit traits of bloom, ground skin color, blush intensity, beak shape, and pulp color.

Systems genetics reveals a transcriptional network associated with susceptibility in the maize-grey leaf spot pathosystem.

Abstract: Table S1. Co-expression module membership of all 19,281 reporters and correlation of reporter expression with GLS disease scores across 100 RILs of the CML444 X SC Malawi population.

The development and use of a molecular model for soybean maturity groups

Abstract: Achieving appropriate maturity in a target environment is essential to maximizing crop yield potential In soybean [Glycine max (L) Merr], the time to maturity is largely dependent on developmental response to dark periods Once the critical photoperiod is reached, flowering is initiated and reproductive development proceeds Therefore, soybean adaptation has been attributed to genetic changes and natural or artificial selection to optimize plant development in specific, narrow latitudinal ranges In North America, these regions have been classified into twelve maturity groups (MG), with lower MG being shorter season than higher MG Growing soybean lines not adapted to a particular environment typically results in poor growth and significant yield reductions The objective of this study was to develop a molecular model for soybean maturity based on the alleles underlying the major maturity loci: E1, E2, and E3 We determined the allelic variation and diversity of the E maturity genes in a large collection of soybean landraces, North American ancestors, Chinese cultivars, North American cultivars or expired Plant Variety Protection lines, and private-company lines The E gene status of accessions in the USDA Soybean Germplasm Collection with SoySNP50K Beadchip data was also predicted We determined the E allelic combinations needed to adapt soybean to different MGs in the United States (US) and discovered a strong signal of selection for E genotypes released in North America, particularly the US and Canada The E gene maturity model proposed will enable plant breeders to more effectively transfer traits into different MGs and increase the overall efficiency of soybean breeding in the US and Canada The powerful yet simple selection strategy for increasing soybean breeding efficiency can be used alone or to directly enhance genomic prediction/selection schemes The results also revealed previously unrecognized aspects of artificial selection in soybean imposed by soybean breeders based on geography that highlights the need for plant breeding that is optimized for specific environments

Breeding for cuticle-associated traits in crop species: traits, targets, and strategies.

Abstract: Improving crop productivity and quality while promoting sustainable agriculture have become major goals in plant breeding The cuticle is a natural film covering the aerial organs of plants and consists of lipid polyesters covered and embedded with wax The cuticle protects plants against water loss and pathogens and affects traits with strong impacts on crop quality such as, for horticultural crops, fruit brightness, cracking, russeting, netting, and shelf life Here we provide an overview of the most important cuticle-associated traits that can be targeted for crop improvement To date, most studies on cuticle-associated traits aimed at crop breeding have been done on fleshy fruits Less information is available for staple crops such as rice, wheat or maize Here we present new insights into cuticle formation and properties resulting from the study of genetic resources available for the various crop species Our review also covers the current strategies and tools aimed at exploiting available natural and artificially induced genetic diversity and the technologies used to transfer the beneficial alleles affecting cuticle-associated traits to commercial varieties

Gene Editing in Polyploid Crops: Wheat, Camelina, Canola, Potato, Cotton, Peanut, Sugar Cane, and Citrus

Abstract: Polyploid crops make up a significant portion of the major food and fiber crops of the world and include wheat, potato, cotton, apple, peanut, citrus, and brassica oilseeds such as rape, canola, and Camelina. The presence of three sets of chromosomes in triploids, four sets in tetraploids, and six sets in hexaploids present significant challenges to conventional plant breeding and, potentially, to efficient use of rapidly emerging gene and genome-editing systems such as zinc finger nucleases, single-stranded oligonucleotides, TALE effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9). However, recent studies with each of these techniques in several polyploid crops have demonstrated facile editing of some or all of the genes targeted for modification on homeologous chromosomes. These modifications have allowed improvements in food nutrition, seed oil composition, disease resistance, weed protection, plant breeding procedures, and food safety. Plants and plant products exhibiting useful new traits created through gene editing but lacking foreign DNA may face reduced regulatory restrictions. Such plants can be obtained either by simply selecting for null segregants that have lost their editing transgenes during plant breeding or, even more attractively, by delivery of biodegradable Cas9/sgRNA ribonucleoprotein complexes (i.e., no DNA) into plant cells where they are expressed only transiently but allow for efficient gene editing-a system that has been recently demonstrated in at least two polyploid crops. Such systems that create precise mutations but leave no transgene footprint hold potential promise for assisting with the elimination or great diminution of regulatory processes that presently burden approvals of conventional transgenic crops.

GWAS for plant growth stages and yield components in spring wheat (Triticum aestivum L.) harvested in three regions of Kazakhstan

Abstract: Spring wheat is the largest agricultural crop grown in Kazakhstan with an annual sowing area of 12 million hectares in 2016. Annually, the country harvests around 15 million tons of high quality grain. Despite environmental stress factors it is predicted that the use of new technologies may lead to increases in productivity from current levels of 1.5 to up to 3 tons per hectare. One way of improving wheat productivity is by the application of new genomic oriented approaches in plant breeding projects. Genome wide association studies (GWAS) are emerging as powerful tools for the understanding of the inheritance of complex traits via utilization of high throughput genotyping technologies and phenotypic assessments of plant collections. In this study, phenotyping and genotyping data on 194 spring wheat accessions from Kazakhstan, Russia, Europe, and CIMMYT were assessed for the identification of marker-trait associations (MTA) of agronomic traits by using GWAS. Field trials in Northern, Central and Southern regions of Kazakhstan using 194 spring wheat accessions revealed strong correlations of yield with booting date, plant height, biomass, number of spikes per plant, and number of kernels per spike. The accessions from Europe and CIMMYT showed high breeding potential for Southern and Central regions of the country in comparison with the performance of the local varieties. The GGE biplot method, using average yield per plant, suggested a clear separation of accessions into their three breeding origins in relationship to the three environments in which they were evaluated. The genetic variation in the three groups of accessions was further studied using 3245 polymorphic SNP (single nucleotide polymorphism) markers. The application of Principal Coordinate analysis clearly grouped the 194 accessions into three clades according to their breeding origins. GWAS on data from nine field trials allowed the identification of 114 MTAs for 12 different agronomic traits. Field evaluation of foreign germplasm revealed its poor yield performance in Northern Kazakhstan, which is the main wheat growing region in the country. However, it was found that EU and CIMMYT germplasm has high breeding potential to improve yield performance in Central and Southern regions. The use of Principal Coordinate analysis clearly separated the panel into three distinct groups according to their breeding origin. GWAS based on use of the TASSEL 5.0 package allowed the identification of 114 MTAs for twelve agronomic traits. The study identifies a network of key genes for improvement of yield productivity in wheat growing regions of Kazakhstan.

Genome wide association analysis of cold tolerance at germination in temperate japonica rice (Oryza sativa L.) varieties.

Abstract: A pool of 200 traditional, landraces and modern elite and old cultivars of rice, mainly japonica varieties adapted to temperate regions, have been used to perform a genome wide association study to detect chromosome regions associated to low temperature germination (LTG) regulation using a panel of 1672 SNP markers. Phenotyping was performed by determining growth rates when seeds were germinated at 25° and 15°C in order to separate the germination vigorousness from cold tolerance effects. As expected, the ability to produce viable seedlings varied widely among rice cultivars and also depended greatly on temperature. Furthermore, we observed a differential response during seed germination and in coleoptile elongation. Faster development at 15°C was observed in seeds from varieties traditionally used as cold tolerant parents by breeders, along with other potentially useful cultivars, mainly of Italian origin. When phenotypic data were combined with the panel of SNPs for japonica rice cultivars, significant associations were detected for 31 markers: 7 were related to growth rate at 25°C and 24 to growth rates at 15°. Among the latter, some chromosome regions were associated to LTG while others were related to coleoptile elongation. Individual effects of the associated markers were low, but by combining favourable alleles in a linear regression model we estimated that 27 loci significantly explained the observed phenotypic variation. From these, a core panel of 13 markers was selected and, furthermore, two wide regions of chromosomes 3 and 6 were consistently associated to rice LTG. Varieties with higher numbers of favourable alleles for the panels of associated markers significantly correlated with increased phenotypic values at both temperatures, thus corroborating the utility of the tagged markers for marker assisted selection (MAS) when breeding japonica rice for LTG.

Sources of resistance and susceptibility to Septoria tritici blotch of wheat.

Abstract: An association genetics analysis was conducted to investigate the genetics of resistance to Septoria tritici blotch, caused by the fungus Zymoseptoria tritici (alternatively Mycosphaerella graminicola), in cultivars and breeding lines of wheat (Triticum aestivum) used in the UK between 1860 and 2000. The population was tested with Diversity Array Technology (DArT) and simple-sequence repeat (SSR or microsatellite) markers. The lines formed a single population with no evidence for subdivision, because there were several common ancestors of large parts of the pedigree. Quantitative trait loci (QTLs) controlling Septoria resistance were postulated on 11 chromosomes, but 38% of variation was not explained by the identified QTLs. Calculation of best linear unbiased predictions (BLUPs) identified lineages of spring and winter wheat carrying different alleles for resistance and susceptibility. Abundant variation in Septoria resistance may be exploited by crossing well-adapted cultivars in different lineages to achieve transgressive segregation and thus breed for potentially durable quantitative resistance, whereas phenotypic selection for polygenic quantitative resistance should be effective in breeding cultivars with increased resistance. The most potent allele reducing susceptibility to Septoria, on chromosome arm 6AL, was associated with reduced leaf size. Genes which increase susceptibility to Septoria may have been introduced inadvertently into UK wheat breeding programmes from cultivars used to increase yield, rust resistance and eyespot resistance between the 1950s and 1980s. This indicates the need to consider trade-offs in plant breeding when numerous traits are important and to be cautious about the use of non-adapted germplasm.

Genetic Parameters and the Impact of Off-Types for Theobroma cacao L. in a Breeding Program in Brazil.

Abstract: Breeding programs of cacao (Theobroma cacao L.) trees share the many challenges of breeding long-living perennial crops, and genetic progress is further constrained by both the limited understanding of the inheritance of complex traits and the prevalence of technical issues, such as mislabeled individuals (off-types). To better understand the genetic architecture of cacao, in this study, 13 years of phenotypic data collected from four progeny trials in Bahia, Brazil were analyzed jointly in a multisite analysis. Three separate analyses (multisite, single site with and without off-types) were performed to estimate genetic parameters from statistical models fitted on 10 important agronomic traits (yield, seed index, pod index, % healthy pods, % pods infected with phytophthora, % pods infected with witches broom, % of pods other loss, vegetative brooms, diameter and tree height). Genetic parameters were estimated along with variance components and heritabilities from the multisite analysis, and a trial was fingerprinted with low-density SNP markers to determine the impact of off-types on estimations. Heritabilities ranged from 0.37-0.64 for yield and its components and from 0.02-0.16 for disease resistance traits. A weighted index was used to make selections for clonal evaluation. The impact of off-types to breeding progress in cacao was assessed for the first time. Even when present at less than 5% of the total population, off-types resulted in a 41% difference in estimated genetic gains for yield, altered selections by 48%, and impacted heritability estimations for nine of the 10 traits analyzed. These results show that in a mixed model analysis, even a low level of pedigree error can significantly alter estimations of genetic parameters and selections in a breeding program.

Accuracy of within‐ and among‐family genomic prediction in triticale

Abstract: Genomic prediction has emerged as a powerful genomic tool to assist breeding of complex traits. In this study, we employed a population of 647 triticale doubled haploid lines derived from four families to assess the potential of this approach for triticale breeding. All lines were phenotyped for grain yield, thousand-kernel weight, biomass yield, plant height, frost tolerance and Fusarium head blight resistance. The obtained prediction accuracies were moderate to high and consisted to varying degrees of within- and among-family variance, in line with the different degrees of phenotypic differences between family means. The prediction accuracy within individual families also varied with the genetic complexity of the traits and was generally highest based on effect estimation with lines from the respective family, whereas the prediction accuracy decreased with decreasing relatedness among the families. Taken together, our results illustrate the potential of genomic prediction to increase selection gain in triticale breeding, but the composition of the training set is of utmost importance, and consequently, the implementation of this approach in applied breeding programmes is not straightforward.

Phenotypic and molecular characterization of sweet sorghum accessions for bioenergy production.

Abstract: Sweet sorghum [Sorghum bicolor (L.) Moench] is a type of cultivated sorghum characterized by the accumulation of high levels of sugar in the stems and high biomass accumulation, making this crop an important feedstock for bioenergy production. Sweet sorghum breeding programs that focus on bioenergy have two main goals: to improve quantity and quality of sugars in the juicy stem and to increase fresh biomass productivity. Genetic diversity studies are very important for the success of a breeding program, especially in the early stages, where understanding the genetic relationship between accessions is essential to identify superior parents for the development of improved breeding lines. The objectives of this study were: to perform phenotypic and molecular characterization of 100 sweet sorghum accessions from the germplasm bank of the Embrapa Maize and Sorghum breeding program; to examine the relationship between the phenotypic and the molecular diversity matrices; and to infer about the population structure in the sweet sorghum accessions. Morphological and agro-industrial traits related to sugar and biomass production were used for phenotypic characterization, and single nucleotide polymorphisms (SNPs) were used for molecular diversity analysis. Both phenotypic and molecular characterizations revealed the existence of considerable genetic diversity among the 100 sweet sorghum accessions. The correlation between the phenotypic and the molecular diversity matrices was low (0.35), which is in agreement with the inconsistencies observed between the clusters formed by the phenotypic and the molecular diversity analyses. Furthermore, the clusters obtained by the molecular diversity analysis were more consistent with the genealogy and the historic background of the sweet sorghum accessions than the clusters obtained through the phenotypic diversity analysis. The low correlation observed between the molecular and the phenotypic diversity matrices highlights the complementarity between the molecular and the phenotypic characterization to assist a breeding program.

Evaluation of Genetic Diversity and Host Resistance to Stem Rust in USDA NSGC Durum Wheat Accessions

Abstract: The USDA-ARS National Small Grains Collection (NSGC) maintains germplasm representing global diversity of small grains and their wild relatives. To evaluate the utility of the NSGC durum wheat ( L. ssp. ) accessions, we assessed genetic diversity and linkage disequilibrium (LD) patterns in a durum core subset containing 429 lines with spring growth habit originating from 64 countries worldwide. Genetic diversity estimated using wheat single-nucleotide polymorphism (SNP) markers showed considerable diversity captured in this collection. Average LD decayed over a genetic distance to within 3 cM at = 0.2, with a fast LD decay for markers linked at >5 cM. We evaluated accessions for resistance to wheat stem rust, caused by a fungal pathogen, Pers. Pers. f. sp. Eriks. and E. Henn (), using races from both eastern Africa and North America, at seedling and adult plant stages. Five accessions were identified as resistant to all stem rust pathogen races evaluated. Genome-wide association analysis detected 17 significant associations at the seedling stage with nine likely corresponding to , , and and the remaining potentially being novel genes located on six chromosomes. A higher frequency of resistant accessions was found at the adult plant stage than at the seedling stage. However, few significant associations were detected possibly a result of strong G × E interactions not properly accounted for in the mixed model. Nonetheless, the resistant accessions identified in this study should provide wheat breeders with valuable resources for improving stem rust resistance.

QTL controlling grain filling under terminal drought stress in a set of wild barley introgression lines.

Abstract: Drought is a major abiotic stress impeding the yield of cereal crops globally. Particularly in Mediterranean environments, water becomes a limiting factor during the reproductive developmental stage, causing yield losses. The wild progenitor of cultivated barley Hordeum vulgare ssp spontaneum (Hsp) is a potentially useful source of drought tolerance alleles. Wild barley introgression lines like the S42IL library may facilitate the introduction of favorable exotic alleles into breeding material. The complete set of 83 S42ILs was genotyped with the barley 9k iSelect platform in order to complete genetic information obtained in previous studies. The new map comprises 2,487 SNPs, spanning 989.8 cM and covering 94.5% of the Hsp genome. Extent and positions of introgressions were confirmed and new information for ten additional S42ILs was collected. A subset of 49 S42ILs was evaluated for drought response in four greenhouse experiments. Plants were grown under well-watered conditions until ten days post anthesis. Subsequently drought treatment was applied by reducing the available water. Several morphological and harvest parameters were evaluated. Under drought treatment, trait performance was reduced. However, there was no interaction effect between genotype and treatment, indicating that genotypes, which performed best under control treatment, also performed best under drought treatment. In total, 40 QTL for seven traits were detected in this study. For instance, favorable Hsp effects were found for thousand grain weight (TGW) and number of grains per ear under drought stress. In particular, line S42IL-121 is a promising candidate for breeding improved malting cultivars, displaying a TGW, which was increased by 17% under terminal drought stress due to the presence of an unknown wild barley QTL allele on chromosome 4H. The introgression line showed a similar advantage in previous field experiments and in greenhouse experiments under early drought stress. We, thus, recommend using S42IL-121 in barley breeding programs to enhance terminal drought tolerance.

Characterization of the Wheat Leaf Metabolome during Grain Filling and under Varied N-Supply.

Abstract: Progress in improving crop growth is an absolute goal despite the influence multifactorial components have on crop yield and quality. An Avalon x Cadenza doubled-haploid wheat mapping population was used to study the leaf metabolome of field grown wheat at weekly intervals during the time in which the canopy contributes to grain filling, i.e. from anthesis to five weeks post anthesis. Wheat was grown under four different nitrogen supplies reaching from residual soil N to a luxury over-fertilization (0, 100, 200, and 350 kg N ha-1). Four lines from a segregating doubled haploid population derived of a cross of the wheat elite cvs. Avalon and Cadenza were chosen as they showed pairwise differences in either N utilization efficiency (NUtE) or senescence timing. 108 annotated metabolites of primary metabolism and ions were determined. The analysis did not provide genotype specific markers because of a remarkable stability of the metabolome between lines. We speculate that the reason for failing to identify genotypic markers might be due to insufficient genetic diversity of the wheat parents and/or the known tendency of plants to keep metabolome homeostasis even under adverse conditions through multiple adaptations and rescue mechanism. The data, however, provided a consistent catalogue of metabolites and their respective responses to environmental and developmental factors and may bode well for future systems biology approaches, and support plant breeding and crop improvement.

Combining ability of highland tropic adapted potato for tuber yield and yield components under drought

Abstract: Recurrent drought and late blight disease are the major factors limiting potato productivity in the northwest Ethiopian highlands. Incorporating drought tolerance and late blight resistance in the same genotypes will enable the development of cultivars with high and stable yield potential under erratic rainfall conditions. The objectives of this study were to assess combining ability effects and gene action for tuber yield and traits related to drought tolerance in the International Potato Centre's (CIP's) advanced clones from the late blight resistant breeding population B group 'B3C2' and to identify promising parents and families for cultivar development. Sixteen advanced clones from the late blight resistant breeding population were crossed in two sets using the North Carolina Design II. The resulting 32 families were evaluated together with five checks and 12 parental clones in a 7 x 7 lattice design with two water regimes and two replications. The experiment was carried out at Adet, in northwest Ethiopia under well-watered and water stressed conditions with terminal drought imposed from the tuber bulking stage. The results showed highly significant differences between families, checks, and parents for growth, physiological, and tuber yield related traits. Traits including marketable tuber yield, marketable tuber number, average tuber weight and groundcover were positively correlated with total tuber yield under both drought stressed and well-watered conditions. Plant height was correlated with yield only under drought stressed condition. GCA was more important than SCA for total tuber yield, marketable tuber yield, average tuber weight, plant height, groundcover, and chlorophyll content under stress. This study identified the parents with best GCA and the combinations with best SCA effects, for both tuber yield and drought tolerance related traits. The new population is shown to be a valuable genetic resource for variety selection and improvement of potato's adaptation to the drought prone areas in northwest Ethiopia and similar environments.