Elite Breeding Populations Research Articles

Improvement of Forage Nutritive Quality of Alfalfa and Red Clover through Plant Breeding

Alfalfa and red clover are important perennial legumes for the production of high-quality fodder. The improvement of the forage quality of legumes is one of the strategic goals of breeding programs. Variation in quality traits (protein content (CP), neutral detergent fiber content (NDF), and acid detergent fiber content (ADF)) and relative feed value (RFV) among seven cultivars and 39 elite breeding populations of alfalfa and red clover was evaluated in the study. Significant differences were determined among the investigated cultivars/populations. Alfalfa populations L-8, 10, 12, 15, and 20 were characterized by a high CP content (up to 23.47%) and/or low NDF and ADF contents. The highest CP content in red clover was recorded in population CD-18 (21.89%), while the lowest NDF and ADF contents were determined in populations CD-19 and CD-4, respectively. High RFV was determined in alfalfa populations L-10, 12, 20, 15, 16, 8, 11, and 17 (prime fodder), and in red clover populations CD-4, 8, 16, 14, and 19 (premium-quality fodder). The identified superior alfalfa and red clover populations will be used to improve the nutritional value of forage crops in our breeding program, which will lead to the release of novel cultivars with improved forage quality.

Performance of 16 Stevia rebaudiana seed cultigens for glycosides and yield in North Carolina

Currently, stevia (Stevia rebaudiana Bertoni) seeds are available to growers from many sources, but the origin of these populations is often unknown. Since stevia is a natural outcrosser, populations are heterozygous and heterogeneous. We were interested to characterize germplasm from 16 sources of stevia seeds for traits including yield, glycosides, and plant morphology, and then identify trait correlations. The cultigens evaluated were obtained from garden seed companies and commercial sources, and the trials were conducted for two years at two field locations. To quantify plant morphological traits, objective measurements were collected at two intervals to determine stem height, branching width, and leaf area. In addition, we screened for lodging and disease resistance, and yield before flowering stage. The cultigens tested were highly variable for yield and steviol glycosides, suggesting that a diverse genetic base is found among the population which is readily available to growers and breeders. High-yielding cultigens for biomass and glycoside concentration were identified. Cultigens with the highest yield and stability over years were seed-derived progeny from ‘Katupyry’, sourced from Stevia Store, and represent genetics useful in breeding for increased biomass. Cultigens with the highest glycoside level were NC-1003 and NC-1022, seed grown from Seed Savers, and could be used to improve desirable glycosides. This study highlights readily available seed cultigens that can be used to develop elite breeding populations.

Optimized breeding strategies to harness genetic resources with different performance levels

BackgroundThe narrow genetic base of elite germplasm compromises long-term genetic gain and increases the vulnerability to biotic and abiotic stresses in unpredictable environmental conditions. Therefore, an efficient strategy is required to broaden the genetic base of commercial breeding programs while not compromising short-term variety release. Optimal cross selection aims at identifying the optimal set of crosses that balances the expected genetic value and diversity. We propose to consider genomic selection and optimal cross selection to recurrently improve genetic resources (i.e. pre-breeding), to bridge the improved genetic resources with elites (i.e. bridging), and to manage introductions into the elite breeding population. Optimal cross selection is particularly adapted to jointly identify bridging, introduction and elite crosses to ensure an overall consistency of the genetic base broadening strategy.ResultsWe compared simulated breeding programs introducing donors with different performance levels, directly or indirectly after bridging. We also evaluated the effect of the training set composition on the success of introductions. We observed that with recurrent introductions of improved donors, it is possible to maintain the genetic diversity and increase mid- and long-term performances with only limited penalty at short-term. Considering a bridging step yielded significantly higher mid- and long-term genetic gain when introducing low performing donors. The results also suggested to consider marker effects estimated with a broad training population including donor by elite and elite by elite progeny to identify bridging, introduction and elite crosses.ConclusionResults of this study provide guidelines on how to harness polygenic variation present in genetic resources to broaden elite germplasm.

Quantitative trait loci for sorghum grain morphology and quality traits: Toward breeding for a traditional food preparation of West-Africa

One of the most frequently consumed sorghum food in Mali is a thick porridge, known as tô. Many grain traits contribute to its firmness and color, which are the most important qualities for consumers. These traits are related to chemical composition, physical properties, but also grain size, shape, glume adherence and color, pericarp thickness, or the presence of a testa. Quantitative trait loci for tô consistency, tô color, 16 grain traits, as well as day to flowering and grain yield, were investigated in two elite breeding populations, involved in a marker assisted selection program. A total of 51 and 71 QTLs were detected for P114 and P118, respectively. Several QTLs with high R2 corresponded to major genes segregating in the populations such as the Z gene for pericarp thickness, the B2 and B1 genes for testa presence, the P gene for anthocyanin, and a QTL for flowering time. Many QTLs with moderate effect were detected for grain attributes associated to tô quality, without showing antagonism between grain quality and yield. The results of this study will contribute to producing new varieties combining grain productivity and grain quality favorable alleles, through the use of marker assisted selection.

Speed breeding for multiple quantitative traits in durum wheat

BackgroundPlant breeding requires numerous generations to be cycled and evaluated before an improved cultivar is released. This lengthy process is required to introduce and test multiple traits of interest. However, a technology for rapid generation advance named ‘speed breeding’ was successfully deployed in bread wheat (Triticum aestivum L.) to achieve six generations per year while imposing phenotypic selection for foliar disease resistance and grain dormancy. Here, for the first time the deployment of this methodology is presented in durum wheat (Triticum durum Desf.) by integrating selection for key traits, including above and below ground traits on the same set of plants. This involved phenotyping for seminal root angle (RA), seminal root number (RN), tolerance to crown rot (CR), resistance to leaf rust (LR) and plant height (PH). In durum wheat, these traits are desirable in environments where yield is limited by in-season rainfall with the occurrence of CR and epidemics of LR. To evaluate this multi-trait screening approach, we applied selection to a large segregating F2 population (n = 1000) derived from a bi-parental cross (Outrob4/Caparoi). A weighted selection index (SI) was developed and applied. The gain for each trait was determined by evaluating F3 progeny derived from 100 ‘selected’ and 100 ‘unselected’ F2 individuals.ResultsTransgressive segregation was observed for all assayed traits in the Outrob4/Caparoi F2 population. Application of the SI successfully shifted the population mean for four traits, as determined by a significant mean difference between ‘selected’ and ‘unselected’ F3 families for CR tolerance, LR resistance, RA and RN. No significant shift for PH was observed.ConclusionsThe novel multi-trait phenotyping method presents a useful tool for rapid selection of early filial generations or for the characterization of fixed lines out-of-season. Further, it offers efficient use of resources by assaying multiple traits on the same set of plants. Results suggest that when performed in parallel with speed breeding in early generations, selection will enrich recombinant inbred lines with desirable alleles and will reduce the length and number of years required to combine these traits in elite breeding populations and therefore cultivars.

Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement.

To address the multiple challenges to food security posed by global climate change, population growth and rising incomes, plant breeders are developing new crop varieties that can enhance both agricultural productivity and environmental sustainability. Current breeding practices, however, are unable to keep pace with demand. Genomic selection (GS) is a new technique that helps accelerate the rate of genetic gain in breeding by using whole-genome data to predict the breeding value of offspring. Here, we describe a new GS model that combines RR-BLUP with markers fit as fixed effects selected from the results of a genome-wide-association study (GWAS) on the RR-BLUP training data. We term this model GS + de novo GWAS. In a breeding population of tropical rice, GS + de novo GWAS outperformed six other models for a variety of traits and in multiple environments. On the basis of these results, we propose an extended, two-part breeding design that can be used to efficiently integrate novel variation into elite breeding populations, thus expanding genetic diversity and enhancing the potential for sustainable productivity gains.

Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa).

Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.

Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping.

Plant breeding programs aim to develop cultivars with high adaptability to the specific conditions in a local region. As a result, unique genes and gene combinations have been accumulated in local elite breeding populations during the long history of plant breeding. Genetic analyses on such genes and combinations may be useful for developing new cultivars with more-desirable agronomic traits. Here, we attempted to detect quantitative trait loci (QTL) for rice blast resistance (BR) using a local breeding rice population from Hokkaido, Japan. Using genotyping data on single nucleotide polymorphisms and simple sequence repeat markers distributed throughout the whole genomic region, we detected genetic regions associated with phenotypic variation in BR by a genome-wide association mapping study (GWAS). An additional association analysis using other breeding cultivars verified the effect and inheritance of the associated region. Furthermore, the existence of a gene for BR in the associated region was confirmed by QTL mapping. The results from these studies enabled us to estimate potential of the Hokkaido rice population as a gene pool for improving BR. The results of this study could be useful for developing novel cultivars with vigorous BR in rice breeding programs.

Molecular characterization of Spanish Prunus avium plus trees

Aim of the study: The Breeding Program of wild cherry (Prunus avium) developed by Lourizán Forest Research Center (NW Spain), aims for the creation of the Main Breeding Population, that is formed by a large number of plus trees and for obtaining an Elite Population generated from controlled crosses of a number of plus trees selected by, at least, one trait of economic importance. The aim of this study was to genotype 131 accessions of Prunus avium plus trees, included in the breeding program.Area of study: The Prunus avium plus trees are located in the North, Northwest and Central Spain.Material and Methods: The Prunus avium plus trees were genotyped with nine microsatellites. Several genetic parameters were calculated. Genetic data were analyzed with STRUCTURE and the genetic distance between the plus trees were calculated.Main results: A total of 122 multilocus genotypes were detected. Several accessions with the same genotype were identified, which could be due to clonality or to labelling errors. The nine microsatellites are useful for identifying individuals because the combined probability of identity was low (PI = 5.19X10-9). Bayesian methods detected two genetic clusters in the sampled plus trees.Research highlights: The unique genotypes identified in this work are suitable for being included in the elite breeding population for economic traits.Keywords: Prunus avium; breeding program; microsatellite; genetic distance.

Genome-wide association mapping of three important traits using bread wheat elite breeding populations

The exponential development of molecular markers enables a more effective study of the genetic architecture of traits of economic importance, like test weight in wheat (Triticum aestivum L.), for which a high value is desired by most end-users. The association mapping (AM) method now allows more precise exploration of the entire genome. AM requires populations with substantial genetic variability of the traits of interest. The breeding lines at the end of a selection cycle, characterized for numerous traits, represent a potentially useful population for AM studies. Using three elite line populations, selected by several breeders and genotyped with about 2,500 Diversity Arrays Technology markers, several associations were identified between these markers and test weight, grain yield and heading date. To minimize spurious associations, we compared the general linear model and mixed linear model (MLM), which adjust for population structure and kinship differently. The MLM model with the kinship matrix was the most efficient. Finally, elite lines from several breeding programs had sufficient genetic variability to allow for the mapping of several chromosomal regions involved in the variation of three important traits.

A genome-wide association study reveals genes associated with fusarium ear rot resistance in a maize core diversity panel.

Fusarium ear rot is a common disease of maize that affects food and feed quality globally. Resistance to the disease is highly quantitative, and maize breeders have difficulty incorporating polygenic resistance alleles from unadapted donor sources into elite breeding populations without having a negative impact on agronomic performance. Identification of specific allele variants contributing to improved resistance may be useful to breeders by allowing selection of resistance alleles in coupling phase linkage with favorable agronomic characteristics. We report the results of a genome-wide association study to detect allele variants associated with increased resistance to Fusarium ear rot in a maize core diversity panel of 267 inbred lines evaluated in two sets of environments. We performed association tests with 47,445 single-nucleotide polymorphisms (SNPs) while controlling for background genomic relationships with a mixed model and identified three marker loci significantly associated with disease resistance in at least one subset of environments. Each associated SNP locus had relatively small additive effects on disease resistance (±1.1% on a 0–100% scale), but nevertheless were associated with 3 to 12% of the genotypic variation within or across environment subsets. Two of three identified SNPs colocalized with genes that have been implicated with programmed cell death. An analysis of associated allele frequencies within the major maize subpopulations revealed enrichment for resistance alleles in the tropical/subtropical and popcorn subpopulations compared with other temperate breeding pools.

Sustainable plant breeding

AbstractPlant breeders disrupt Hardy–Weinberg equilibrium through selection, non‐random mating, drift, migration and mutation. Sustainable plant breeding can be defined as productive and competitive breeding that is achieved without loss of genetic diversity in the elite breeding population during the professional career of the breeder. Breeding is often productive but not sustainable. From 1974 to 2000, the animal breeding programme Meatlinc in the United Kingdom had effective population size of 95, population inbreeding of 0.19% per year and generation interval of 2.15 years. Genetic progress in Meatlinc tripled in the 8 years following introduction of best linear unbiased prediction (BLUP) selection (based on the information from relatives) in 1992. Canola breeding in Australia from 1970 to 2000 had longer generation interval (6 years), smaller effective population size (<11) and higher rates of inbreeding (>0.7% per year). BLUP selection in canola was first reported in 2010. Neither programme replaced genetic diversity lost through selection and drift. Most breeding programmes violate conditions of the infinitesimal model, thereby reducing predictability of selection, but breeders can minimize these limitations to sustainable plant breeding.

Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing.

BackgroundAlfalfa, a perennial, outcrossing species, is a widely planted forage legume producing highly nutritious biomass. Currently, improvement of cultivated alfalfa mainly relies on recurrent phenotypic selection. Marker assisted breeding strategies can enhance alfalfa improvement efforts, particularly if many genome-wide markers are available. Transcriptome sequencing enables efficient high-throughput discovery of single nucleotide polymorphism (SNP) markers for a complex polyploid species.ResultThe transcriptomes of 27 alfalfa genotypes, including elite breeding genotypes, parents of mapping populations, and unimproved wild genotypes, were sequenced using an Illumina Genome Analyzer IIx. De novo assembly of quality-filtered 72-bp reads generated 25,183 contigs with a total length of 26.8 Mbp and an average length of 1,065 bp, with an average read depth of 55.9-fold for each genotype. Overall, 21,954 (87.2%) of the 25,183 contigs represented 14,878 unique protein accessions. Gene ontology (GO) analysis suggested that a broad diversity of genes was represented in the resulting sequences. The realignment of individual reads to the contigs enabled the detection of 872,384 SNPs and 31,760 InDels. High resolution melting (HRM) analysis was used to validate 91% of 192 putative SNPs identified by sequencing. Both allelic variants at about 95% of SNP sites identified among five wild, unimproved genotypes are still present in cultivated alfalfa, and all four US breeding programs also contain a high proportion of these SNPs. Thus, little evidence exists among this dataset for loss of significant DNA sequence diversity from either domestication or breeding of alfalfa. Structure analysis indicated that individuals from the subspecies falcata, the diploid subspecies caerulea, and the tetraploid subspecies sativa (cultivated tetraploid alfalfa) were clearly separated.ConclusionWe used transcriptome sequencing to discover large numbers of SNPs segregating in elite breeding populations of alfalfa. Little loss of SNP diversity was evident between unimproved and elite alfalfa germplasm. The EST and SNP markers generated from this study are publicly available at the Legume Information System ( http://medsa.comparative-legumes.org/) and can contribute to future alfalfa research and breeding applications.

Microsatellite markers reveal Cameroon’s wild oil palm population as a possible solution to broaden the genetic base in the Indonesia-Malaysia oil palm breeding programs

Intensive breeding from a narrow genetic base of the South East Asian oil palm industry has led to limited variation within elite breeding population thereby reducing the rate of future breeding progress. The use of wild genotypes are known to broaden the genetic base of breeding populations because of their high rate of heterozygosity. Historical evidence show that Cameroon has supplied wild genetic material to the major oil palm breeding programmes in the world. The aim of this study was to study the extent of genetic diversity existing in the present Cameroonian oil palm wild population and detectgenotypes which could be used for recombinations in breeding programmes. Thirty nine accessions consisting of five palms each were analysed using 16 simple sequence repeats (SSR) loci. The results show the percentage of polymorphic loci at 96.43% with a mean polymorphic information content (PIC) of 0.60. The number of alleles (Na) was at 4.71 while the effective number of Alleles (Ne) was at 2.30 ± 0.90. Genetic similarity between individuals was very low with genetic similarity (I) at 0.29. The high values formean expected heterozygosity (He), observed heterozygosity (Ho) and polymorphic loci, suggest this population had a high genetic variability. The use of this molecular data complemented with agro morphological data will greatly enhance new breeding programs in oil palm. Key words: Cameroon wild oil palm, elite breeding population, polymorphic information content (PIC), breeding programmes, simple sequence repeats (SSR) markers, Elaeis guineensis.

Progress towards marker-assisted selection in forages

In developing marker-assisted selection (MAS) for herbage yield and persistence traits in forages, traitlinked markers were tested in elite breeding populations of complex parentage, to identify population-specific marker:trait associations. The effectiveness of these were subsequently evaluated in progeny generated by MAS. In white clover (Trifolium repens), markers detected significant (P

Breeding for hygienic behaviour in honeybees (Apis mellifera) using free-mated nucleus colonies

Gains in hygienic behaviour based on maternal selection of queens were evaluated among four commercial beekeeping operations in northern Alberta, Canada over four generations. While the proportion of breeding colonies expressing the trait increased with each subsequent generation, levels of hygienic behaviour among progeny remained relatively unchanged. Estimated breeding values for the final generation of progeny confirmed only a slight effect of selection; the expected average increase in the removal of frozen brood in the next generation was determined to be 0.17% at 24 h and 0.34% at 48 h. This modest increase may be explained by the low (24 h, h2 = 0.17) to moderate (48 h, h2 = 0.25) heritability of hygienic behaviour in our population. Our work implies that year-to-year comparisons of breeding colonies may not be an accurate predictor of selection gains within honeybee populations and that honey producers in this region may need to focus selection within elite breeding populations.

Accuracy of genomic selection in European maize elite breeding populations

Genomic selection is a promising breeding strategy for rapid improvement of complex traits. The objective of our study was to investigate the prediction accuracy of genomic breeding values through cross validation. The study was based on experimental data of six segregating populations from a half-diallel mating design with 788 testcross progenies from an elite maize breeding program. The plants were intensively phenotyped in multi-location field trials and fingerprinted with 960 SNP markers. We used random regression best linear unbiased prediction in combination with fivefold cross validation. The prediction accuracy across populations was higher for grain moisture (0.90) than for grain yield (0.58). The accuracy of genomic selection realized for grain yield corresponds to the precision of phenotyping at unreplicated field trials in 3-4 locations. As for maize up to three generations are feasible per year, selection gain per unit time is high and, consequently, genomic selection holds great promise for maize breeding programs.

Exploring and Exploiting Genetic Variation from Unadapted Sorghum Germplasm in a Breeding Program

ABSTRACTLoss of genetic diversity in elite breeding populations is often identified as a potential impediment to future genetic gain. The use of diverse unadapted germplasm in breeding has been suggested as one way of combating this problem but often proves impractical, due to the poor performance of progeny produced by crosses between adapted and unadapted parent lines. This study evaluates the effectiveness of a breeding method aimed at utilizing unadapted sorghum [Sorghum bicolor (L.) Moench] germplasm. The method involves producing large BC1F1 populations, using a single elite line as the recurrent parent, and then selecting the resulting progeny for key adaptive traits (e.g., height and flowering time). Populations of 30 to 90 BC1F4 lines derived from 56 unadapted parents were then evaluated in hybrid combination in 21 trials over a 4‐yr period. The unadapted sources included lines with geographic or racial diversity, phenotypic diversity for key traits, elite lines from breeding programs in other countries, and cross‐compatible wild species. Despite strong selection for acceptable height and maturity, considerable genetic variation for grain yield was retained in the populations, with molecular marker analysis indicating an average of 22% of the genome being retained in each line as compared with a theoretical 25% in the absence of selection. In all cases progeny were identified in each population that performed significantly better than the recurrent parent hybrid for grain yield, and in some cases specific adaptation of particular populations was observed. The method we used proved to be an effective way to introduce new alleles from unadapted sorghum germplasm into elite breeding material. The potential of the populations as a resource for nested association mapping to elucidate the architecture of complex traits is discussed.

Generating and maintaining diversity at the elite level in crop breedingThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”

Most breeding programs develop elite genotypes that are well adapted to the normal range of environmental conditions in the target production region. These elite lines have similar essential alleles for desirable end use characteristics, agronomics, disease resistance, and adaptation in the target region. The genetic makeup of these elite lines is complex. Intermating among the elite lines will often produce new variability through recombination with minimal risk of introducing new undesirable features, and is the source of most new cultivars. Eventually, this variation will be exhausted and new alleles must be introduced into the elite breeding population. Introducing desirable alleles from exotic germplasm may "pollute" the elite gene pool with undesirable alleles. Exotic germplasm may also disrupt essential allele combinations for adaptation, quality, and agronomic performance. New desirable alleles from exotic germplasm can be introgressed into an elite population in a systematic way through limited backcrossing with a minimal disturbance to the finely tuned elite background. Combining recurrent selection within elite germplasm with a systematic introgression from exotic germplasm in the recurrent introgressive population enrichment (RIPE) system has created an open-ended, continually improving, and sustainable elite population breeding system, which is simple, effective, and a regular source of new cultivars.

Genetic basis of agronomically important traits in sugar beet (Beta vulgaris L.) investigated with joint linkage association mapping

Epistatic interactions may contribute substantially to the hybrid performance of sugar beet. The main goal of our study was to dissect the genetic basis of eight important physiological and agronomic traits using two different biometrical models for joint linkage association mapping. A total of 197 genotypes of an elite breeding population were evaluated in multi-location trials and fingerprinted with 194 SNP markers. Two different statistical models were used for the genome-wide scan for marker-trait associations: Model A, which corrects for the genetic background with markers as cofactors and Model B, which additionally models a population effect. Based on the extent of linkage disequilibrium in the parental population, we estimated that for a genome-wide scan at least 100 equally spaced markers are necessary. We mapped across the eight traits 39 QTL for Model A and 22 for Model B. Only 11% of the total number of QTL were identified based on Models A and B, which indicates that both models are complementary. Epistasis was detected only for two out of the eight traits, and contributed only to a minor extent to the genotypic variance. This low relevance of epistasis implies that in sugar beet breeding the prediction of performance of three-way hybrids is feasible with high accuracy based on the means of their single crosses.