Accessions In Germplasm Collections Research Articles

HERRAMIENTAS COMPLEMENTARIAS UTILIZADAS EN EL PROGRAMA DE MEJORAMIENTO DE ARVEJA (Pisum sativum L.) DE LA UNIVERSIDAD NACIONAL DE ROSARIO

Conventional breeding can be complemented by different strategies that increase the efficiency of the methodologies and the current rate of increase in yields in order to meet demand. The use of molecular markers with the aim of developing linkage maps of the species, the use of Blup (Best Linear Unbiased Prediction) for an efficient selection of progenitors to hybridize, the use of in vitro culture to artificially increase the number of F1 plants or the use of digital phenotyping for efficient digital characterization that can be performed during the periodic and routine regeneration of accessions in germplasm collections. Key words: Molecular markers, Blup, in vitro culture, digital phenotyping.

Genetic relationships in Saccharum complex germplasm collections based on morphological and molecular markers

and is a cross-pollinator, so information about the genetic relationship between the accessions in germplasm collections is very important for selecting the prospective parent in crossbreeding. This research aims to determine the phylogenetic relationship of 24 Saccharum complex accessions and to verify the grouping of accessions using 37 morphological and three microsatellite molecular markers. Interpretation of morphological and molecular data was obtained from the analysis using the NTYSYpc-2.02i program. The results show that within the 24 accessions analyzed using morphological markers, some accessions did not cluster as the classification at the conservation time. This difference is due to the morphological markers, descriptions of characters that do not appear are considered as the same variables though in different morphological characters, so this increases the value of genetic similarity among accessions analyzed. In contrast, the grouping of molecular markers shows that each accession was grouped according to the classification at the conservation time. These accessions had a low genetic similarity of 0.20 with a broad genetic distance of 0.80. This broad genetic distance indicates that the twenty-four accessions have a distant genetic relationship with one another, so that the genetic diversity of these accessions is relatively high. The high genetic diversity in germplasm collections improves its potential as a crossing parent to obtain a high heterosis effect.

Development of a minimal KASP marker panel for distinguishing genotypes in apple collections.

Accurate identification of named accessions in germplasm collections is extremely important, especially for vegetatively propagated crops which are expensive to maintain. Thus, an inexpensive, reliable, and rapid genotyping method is essential because it avoids the need for laborious and time-consuming morphological comparisons. Single Nucleotide Polymorphism (SNP) marker panels containing large numbers of SNPs have been developed for many crop species, but such panels are much too large for basic cultivar identification. Here, we have identified a minimum set of SNP markers sufficient to distinguish apple cultivars held in the English and Welsh national collections providing a cheaper and automatable alternative to the markers currently used by the community. We show that SNP genotyping with a small set of well selected markers is equally efficient as microsatellites for the identification of apple cultivars and has the added advantage of automation and reduced cost when screening large numbers of samples.

Bayesian optimization for genomic selection: a method for discovering the best genotype among a large number of candidates.

A new pre-breeding strategy based on an optimization algorithm is proposed and evaluated via simulations. This strategy can find superior genotypes with less phenotyping effort. Genomic prediction is a promising approach to search for superior genotypes among a large number of accessions in germplasm collections preserved in gene banks. When some accessions are phenotyped and genotyped, a prediction model can be built, and the genotypic values of the remaining accessions can be predicted from their marker genotypes. In this study, we focused on the application of genomic prediction to pre-breeding, and propose a novel strategy that would reduce the cost of phenotyping needed to discover better accessions. We regarded the exploration of superior genotypes with genomic prediction as an optimization problem, and introduced Bayesian optimization to solve it. Bayesian optimization, that samples unobserved inputs according to the expected improvement (EI) as a selection criterion, seemed to be beneficial in pre-breeding. The EI depends on the predicted distribution of genotypic values, whereas usual selection depends only on the point estimate. We simulated a search for the best genotype among candidate genotypes and showed that the EI-based strategy required fewer genotypes to identify the best genotype than the usual and random selection strategy. Therefore, Bayesian optimization can be useful for applying genomic prediction to pre-breeding and would reduce the number of phenotyped accessions needed to find the best accession among a large number of candidates.

Concordance between botanical groups and genetic diversity in peanut

The aims of this study were to characterize peanut accessions of germplasm collection of the CCA/UFC and check consistency between the pre-existing botanical groups to estimates of genetic diversity. For this were conducted a trial with 43 accessions of peanut in a randomized block design with three replications. To characterization were used 21 morphological descriptors, where revealed large genetic variation. The mass hundred grains trait showed the main discriminating factors, with relative percentage of 22.1%. The cluster obtained with the linkage complete method, it was possible to view the dendrogram the formation of seven groups based on the Mahalanobis distance. By principal components analysis was identified phenotypic diversity among genotypes. The first three components explained 81% of the total variation. Subsequently, built a three-dimensional scatter chart for access of visualization, eight groups being formed. There was medium magnitude of agreement between the botanical groups and genetic diversity, both by the dendrogram and graphic dispersion proving the dissimilarity between genotypes of different botanic groups. Therefore, crossings between group access botanical Spanish or Valencia with those belonging to the Virginia group should generate segregating populations with high genetic potential.

The wild side of a major crop: soybean's perennial cousins from Down Under.

The accumulation of over 30 years of basic research on the biology, genetic variation, and evolution of the wild perennial relatives of soybean (Glycine max) provides a foundation to improve cultivated soybean. The cultivated soybean and its wild progenitor, G. soja, have a center of origin in eastern Asia and are the only two species in the annual subgenus Soja. Systematic and evolutionary studies of the ca. 30 perennial species of subgenus Glycine, native to Australia, have benefited from the availability of the G. max genomic sequence. The perennial species harbor many traits of interest to soybean breeders, among them resistance to major soybean pathogens such as cyst nematode and leaf rust. New species in the Australian subgenus continue to be described, due to the collection of new material and to insights gleaned through systematic studies of accessions in germplasm collections. Ongoing studies in perennial species focus on genomic regions that contain genes for key traits relevant to soybean breeding. These comparisons also include the homoeologous regions that are the result of polyploidy in the common ancestor of all Glycine species. Subgenus Glycine includes a complex of recently formed allopolyploids that are the focus of studies aimed at elucidating genomic, transcriptomic, physiological, taxonomic, morphological, developmental, and ecological processes related to polyploid evolution. Here we review what has been learned over the past 30 years and outline ongoing work on photosynthesis, nitrogen fixation, and floral biology, much of it drawing on new technologies and resources.

Strategy for exploiting exotic germplasm using genetic, morphological, and environmental diversity: the Aegilops tauschii Coss. example

Hexaploid bread wheat evolved from a rare hybridisation, which resulted in a loss of genetic diversity in the wheat D-genome with respect to the ancestral donor, Aegilops tauschii. Novel genetic variation can be introduced into modern wheat by recreating the above hybridisation; however, the information associated with the Ae. tauschii accessions in germplasm collections is limited, making rational selection of accessions into a re-synthesis programme difficult. We describe methodologies to identify novel diversity from Ae. tauschii accessions that combines Bayesian analysis of genotypic data, sub-species diversity and geographic information that summarises variation in climate and habitat at the collection point for each accession. Comparisons were made between diversity discovered amongst a panel of Ae. tauschii accessions, bread wheat varieties and lines from the CIMMYT synthetic hexaploid wheat programme. The selection of Ae. tauschii accessions based on differing approaches had significant effect on diversity within each set. Our results suggest that a strategy that combines several criteria will be most effective in maximising the sampled variation across multiple parameters. The analysis of multiple layers of variation in ex situ Ae. tauschii collections allows for an informed and rational approach to the inclusion of wild relatives into crop breeding programmes.

Genomics of plant genetic resources: past, present and future

Plant genetic resources (PGR) include cultivars, landraces, wild species closely related to cultivated varieties, breeder's elite lines and mutants. The loss of genetic diversity caused by the practice of agriculture and the availability of genetic information has resulted in a great effort dedicated to the collection of PGR. Prior to the advent of molecular profiling, accessions in germplasm collections were examined based on morphology. The development of molecular techniques now allows a more accurate analysis of large collections. Next-generation sequencing (NGS) with de novo assembly and resequencing has already provided a substantial amount of information, which warrants the coordination of existing databases and their integration into genebanks. Thus, the integration and coordination of genomic data into genebanks is very important and requires an international effort. From the determination of phenotypic traits to the application of NGS to whole genomes, every aspect of genomics will have a great impact not only on PGR conservation, but also on plant breeding programmes.

Evaluating Potential Genetic Gains in Wheat Associated with Stress‐Adaptive Trait Expression in Elite Genetic Resources under Drought and Heat Stress

ABSTRACTWhile genetic resources provide an invaluable gene pool for crop breeding, the majority of accessions in germplasm collections remain uncharacterized and their potential to improve stress adaptation is not quantified. A selection of 25 elite genetic resources for wheat (Triticum aestivum L.) were characterized for agronomic and physiological trait expression in drought‐ and heat‐stressed environments. Under drought, the physiological traits best associated with yield were canopy temperature, associated with water uptake, and carbon isotope discrimination, associated with transpiration efficiency. Under heat stress stomatal conductance, leaf chlorophyll content, and canopy temperature (associated with radiation use efficiency in this environment) were well correlated with yield. Theoretical yield gains based on extrapolating the best trait expression to the highest yielding backgrounds were also estimated. Under drought, the best expression of canopy temperature and carbon isotope discrimination suggested potential yield gains of approximately 10 and 9% above the best yielding cultivars, respectively; under heat stress, canopy temperature and remobilization of stem carbohydrates suggested potential yield gains of approximately 7 and 9%, respectively. Other physiological trait expression was associated with potential yield gains to varying degrees. When considering agronomic traits, the best expression of harvest index suggested yield gains of approximately 14 and 24% in drought and hot environments, respectively, while the combined best expression of both harvest index and final aboveground biomass suggested yield gains of 30 and 34%, respectively. Principal component analysis indicated that many of the physiological traits that were associated with yield and biomass were not strongly associated with each other, suggesting potential cumulative gene action for yield if traits were combined. When comparing trait expression across drought and hot environments, several physiological traits (e.g., canopy temperature) showed closer association with each other than did performance traits, supporting the idea that such stress‐adaptive traits have generic value across stresses.

Evaluation of wheat germplasm from the Madeira and Canary archipelagos using a single molecular marker. A rapid screening method for identification of durum wheat accessions

This work aims to present a rapid and precise screening method of wheat germplasm and identification of durum wheat accessions in germplasm collections. Fifty-two wheat accessions maintained in the ISOPlexis germplasm bank at the Madeira University, Portugal, and 72 accessions from the Centre for Conservation of Crop Biodiversity of Tenerife (CCBAT), Spain, have been screened for their specific ploidy status using the molecular marker Dgas44. We have demonstrated that the Dgas44 sequence is effective in the screening of Madeiran and Canarian wheat accessions. This screening method permitted the detection of 10 and 11 durum accessions among Madeiran and Canarian wheats, accounting for 19.2 and 15.3% of screened collections, respectively. The obtained results have shown a 100% of cases correspondence with the previously performed morphological identification of the Madeiran wheats. It also permitted rectification and clarification of previous classification of some accessions based only on the morphological traits. The PCR based assay was directly applicable to the screening of seeds and was suitable for detecting seed mixtures in accessions. This rapid method has been proven to be a useful tool in gene bank accessions management including verification of their ploidy status and detection of seed lots adulteration.

Análise da diversidade genética entre acessos de banco ativo de germoplasma de algodão

O conhecimento da diversidade genética entre um grupo de genitores é importante no melhoramento, sobretudo na identificação de combinações híbridas de maior heterozigose e maior efeito heterótico e, portanto, na recuperação de genótipos superiores nas gerações segregantes. Os métodos preditivos de diversidade têm sido muito utilizados porque dispensam a obtenção de combinações híbridas entre os genitores e normalmente usam uma medida de similaridade para avaliar a diversidade entre eles. Foram avaliados 221 acessos do banco ativo de germoplasma de algodão da Epamig, por meio da distância euclidiana média e posterior agrupamento dos indivíduos, de modo a permitir escolhas mais apropriadas de genitores para cruzamentos. Para isso foram consideradas 11 características morfológicas e de fibra. Foi detectada grande diversidade genética entre os 221 acessos reunidos em dez grupos distintos. A maior distância euclidiana (4,36) ocorreu entre os acessos S 8186 e T-295-1-1 e a menor (0,25) entre os acessos TX CACES 1-81 e TX CDPS 177.

Variability of Thirteen Isozyme Loci in the USDA Soybean Germplasm Collections

Surveys of variability at loci that condition simply inherited, phenotypically neutral characters can be used to investigate relationships among accessions in germplasm collections. We performed a survey of isozyme variability among 1005 domesticated soybean [Glycine max (L.) Merr.] and 258 wild soybean [G. soja (L.) Siebold & Zucc.] accessions from the USDA soybean germplasm collection. By using eight activity stains, we detected polymorphisms conditioned by 13 isozyme loci. The average gene diversity of the Asian G. max accessions in this study was 0.198, while that of the G. soja accessions was 0.235. The relatively high variability of this set of loci made it possible to investigate relationships among groups of accessions from six diverse geographic regions in Asia: China, India and South‐Central Asia, Japan, Korea, Manchuria‐Siberia, and Southeast Asia. The G. max and G. soja accessions fell into two separate groups, based both on genetic distance and canonical discriminant analysis. Publicly developed soybean cultivars released for production in North America clustered with the G. max accessions from northeast Asia. The group of accessions from India and South‐Central Asia was the G. max group most closely related to the G. soja accessions and may include some primitive agronomic types. The group of G. max accessions from Southeast Asia stood out from the other G. max groups. This difference was due to high frequencies of the Aco3‐b, Dial, and Enp‐a alleles among accessions in Maturity Groups VII through X. The accessions in the later maturity groups may represent a distinct population, relative to the accessions in the earlier maturity groups.

8. Molecular biology and genetic conservation programmes

The techniques of molecular biology will become a standard part of germplasm conservation and exploitation. They are being used to gather information very rapidly about chromosome structure and genetic variation within the major crop species. Genetic maps with hundreds of DNA sequence markers covering the whole genome have already been created for some crops, such as maize, soybean, wheat and potato. Genetic variation is being revealed by the combined use of restriction endonucleases, fractionation of DNA fragments by electrophoresis and investigation of the size of specific allelic fragments. This kind of approach offers new opportunities to assess the extent of genetic variation among accessions in germplasm collections, thereby helping to decide which accessions are essentially duplicates and which should be maintained in a core collection. I recommend that germplasm banks will in the future also contain diagnostic DNA markers for characterizing and screening germplasm. When material from germplasm banks is used in crop plant breeding programmes to transfer specific traits into the crop, the availability of a complete set of molecular markers covering the entire genome makes it straightforward to discover which segments have been transferred and which are essential to maintain, so as to preserve the introduced trait. Germplasm banks are obviously a source of new genetic variation for the molecular geneticist as well as the plant breeder. The isolation of specific alleles determining self-incompatibility from Brassica oleracea accessions for subsequent introduction into oil seed rape is described as an example.