A Modified Roger’s Distance Algorithm for Mixed Quantitative–Qualitative Phenotypes to Establish a Core Collection for Taiwanese Vegetable Soybeans

Vegetable soybeans [Glycine max (L.) Merr.] have characteristics of larger seeds, less beany flavor, tender texture, and green-colored pods and seeds. Rich in nutrients, vegetable soybeans are conducive to preventing neurological disease. Due to the change of dietary habits and increasing health awareness, the demand for vegetable soybeans has increased. To conserve vegetable soybean germplasms in Taiwan, we built a core collection of vegetable soybeans, with minimum accessions, minimum redundancy, and maximum representation. Initially, a total of 213 vegetable soybean germplasms and 29 morphological traits were used to construct the core collection. After redundant accessions were removed, 200 accessions were retained as the entire collection, which was grouped into nine clusters. Here, we developed a modified Roger’s distance for mixed quantitative–qualitative phenotypes to select 30 accessions (denoted as the core collection) that had a maximum pairwise genetic distance. No significant differences were observed in all phenotypic traits (p-values > 0.05) between the entire and the core collections, except plant height. Compared to the entire collection, we found that most traits retained diversities, but seven traits were slightly lost (ranged from 2 to 9%) in the core collection. The core collection demonstrated a small percentage of significant mean difference (3.45%) and a large coincidence rate (97.70%), indicating representativeness of the entire collection. Furthermore, large values in variable rate (149.80%) and coverage (92.5%) were in line with high diversity retained in the core collection. The results suggested that phenotype-based core collection can retain diversity and genetic variability of vegetable soybeans, providing a basis for further research and breeding programs.

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Comparing the efficiency of sampling strategies to establish a representative in the phenotypic-based genetic diversity core collection of orchardgrass (Dactylis glomerata L.)

Czech Journal of Genetics and Plant Breeding ◽

10.17221/9/2012-cjgpb ◽

2013 ◽

Vol 49 (No. 1) ◽

pp. 36-47 ◽

Cited By ~ 4

Author(s):

M. Studnicki ◽

W. Mądry ◽

J. Schmidt

Keyword(s):

Genetic Diversity ◽

Core Collection ◽

Dactylis Glomerata ◽

Sampling Strategy ◽

Sampling Strategies ◽

Core Collections ◽

The Core ◽

Entire Collection ◽

The Mean ◽

Dactylis Glomerata L

Establishing a core collection that represents the genetic diversity of the entire collection with a minimum loss of its original diversity and minimal redundancies is an important problem for gene bank curators and crop breeders. In this paper, we assess the representativeness of the original genetic diversity in core collections consisting of one-tenth of the entire collection obtained according to 23 sampling strategies. The study was performed using the Polish orchardgrass Dactylis glomerata L. germplasm collection as a model. The representativeness of the core collections was validated by the difference of means (MD%) and difference of mean squared Euclidean distance (d‒D%) for the studied traits in the core subsets and the entire collection. In this way, we compared the efficiency of a simple random and 22 (20 cluster-based and 2 direct cluster-based) stratified sampling strategies. Each cluster-based stratified sampling strategy is a combination of 2 clusterings, 5 allocations and 2 methods of sampling in a group. We used the accession genotypic predicted values for 8 quantitative traits tested in field trials. A sampling strategy is considered more effective for establishing core collections if the means of the traits in a core are maintained at the same level as the means in the entire collection (i.e., the mean of MD% in the simulated samples is close to zero) and, simultaneously, when the overall variation in a core collection is greater than in the entire collection (i.e., the mean of d‒D% in the simulated samples is greater than that obtained for the simple random sampling strategy). Both cluster analyses (unweighted pair group method with arithmetic mean UPGMA and Ward) were similarly useful in constructing those sampling strategies capable of establishing representative core collections. Among the allocation methods that are relatively most useful for constructing efficient samplings were proportional and D2 (including variation). Within the Ward clusters, the random sampling was better than the cluster-based sampling, but not within the UPGMA clusters.

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Establishment of a cassava (Manihot esculenta Crantz) core collection based on agro-morphological descriptors

Plant Genetic Resources ◽

10.1017/s1479262112000093 ◽

2012 ◽

Vol 10 (2) ◽

pp. 119-127 ◽

Cited By ~ 6

Author(s):

Ranjana Bhattacharjee ◽

Dominique Dumet ◽

Paul Ilona ◽

Soyode Folarin ◽

Jorge Franco

Keyword(s):

Manihot Esculenta ◽

Core Collection ◽

Phenotypic Diversity ◽

Crop Improvement ◽

International Institute ◽

Environment Interaction ◽

Manihot Esculenta Crantz ◽

Linear Discriminant ◽

The Core ◽

Entire Collection

International Institute of Tropical Agriculture maintains 2544 cassava accessions (Manihot esculenta Crantz) from 28 countries in its field bank. Being vegetatively propagated, this poses challenges in maintenance in terms of cost as well as in labour requirements. A core collection representing the range of phenotypic diversity present in the entire collection would enhance the conservation aspects and increase the potential for its exploitation in crop improvement programmes. The present study aimed to establish a core collection using 40 agro-morphological traits evaluated at two locations using a different number of accessions in each location. To meet the challenges generated by the types of variables and include maximum diversity in the core collection, a sequential strategy based on five major concepts was used: hierarchical multiple factor analysis allowing the mixture of variables of different kinds; three-way analysis that included the effect of genotype × environment interaction in the clustering process; linear discriminant function to assign all those individuals who were included in one location but not in the other to the groups that were generated from the common number of accessions evaluated in both locations; and D-allocation method to select samples from each cluster. The representativeness of the core subset to the entire collection was further estimated by comparing means and variances, range, and distances between accessions. The established cassava core collection consisted of 428 accessions that conserved 15% higher phenotypic diversity with no redundancies. The phenotypic diversity represented in this core collection will be a guide to users of cassava germplasm in their crop improvement programmes.

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Establishment of a core collection of Cynodon based on morphological data

Tropical Grasslands - Forrajes Tropicales ◽

10.17138/tgft(8)203-213 ◽

2020 ◽

Vol 8 (3) ◽

pp. 203-213

Author(s):

C.Q. Huang ◽

T. Long ◽

C.J. Bai ◽

W.Q. Wang ◽

J. Tang ◽

...

Keyword(s):

Mahalanobis Distance ◽

Core Collection ◽

Morphological Data ◽

Phenotypic Traits ◽

Optimal Sampling ◽

Square Root ◽

Sample Distribution ◽

Core Collections ◽

The Core ◽

Preferential Sampling

In a field plot study conducted in Danzhou, Hainan province, China, a total of 537 wild Cynodon accessions from 22 countries and classified into 11 groups according to taxonomy and origin, were characterized in terms of 11 phenotypic traits in order to construct a core collection. For this, the optimal strategy was developed by screening within the following method levels: (i) 7 sampling proportions (5, 10, 15, 20, 25, 30 and 35%); (ii) 3 sampling methods (preferential sampling, deviation sampling and random sampling); (iii) 5 clustering methods [single linkage, completed linkage, median linkage, unweighted pair-group average (UPGMA) and Ward’s method]; (iv) 3 genetic distances (Euclidean distance, Mahalanobis distance and principal component distance); and (v) 3 sampling proportions within groups (simple, logarithmic and square root proportions). Mean difference percentage, variance difference percentage, coincidence rate of range and variation coefficient changing rate were the criteria adopted for evaluating how well the core collection represented the original collection. The correlation between the original and core collections was determined for comparison. The core collections were validated with the sample distribution diagram of the main components. Results showed that the optimal sampling method for constructing a Cynodon core collection was preferential sampling, the optimal sampling proportion being 20%. The optimal sampling proportion within groups was the square root proportion, the optimal genetic distance was Mahalanobis distance and the optimal clustering method was UPGMA. The proposed core collection of Cynodon is composed of 108 accessions; it was constructed following the optimal sampling strategy identified and retained the original collection´s phenotypic diversity, phenotypic trait correlations and phenotypic group structure. Thus, this collection could be considered a representative sample of the entire resource.

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Development of the core collection through advanced maximization strategy with heuristic approach in cashew (Anacardium occidentale L.)

Plant Genetic Resources ◽

10.1017/s1479262118000035 ◽

2018 ◽

Vol 16 (4) ◽

pp. 367-377 ◽

Cited By ~ 1

Author(s):

G. S. Mohana ◽

M. G. Nayak

Keyword(s):

Core Collection ◽

Heuristic Approach ◽

Gene Bank ◽

Morphometric Characters ◽

The Core ◽

Efficient Management ◽

Entire Collection ◽

Validation Parameters ◽

Separate Block ◽

Clustering Approach

AbstractICAR-Directorate of Cashew Research is the nodal agency for conducting cashew research and manages the largest field gene bank in India. Cashew is a perennial tree and needs more land and other resources to maintain accessions. Conservation through seeds is not feasible because of cross-pollination. Tissue culture efforts to regenerate plants from mature explants are not successful. Therefore, efficient management of the filed gene bank particularly utilization requires designation of the core collection representing the spectrum of diversity present in the entire collection. In this study, a relatively new technique, the advanced M strategy with heuristic approach was deployed to develop the core collection. Sixty-eight morphometric characters of 478 accessions were subjected to analysis resulting in the core collection of 49 accessions. Further, another core collection of same number was constituted by K-Means clustering to compare the efficiency of two approaches. The validation parameters like mean difference, variance difference, coincidence rate, variable rate and class coverage among others were employed for comparative analysis. The results of these parameters revealed that the core collection designated by heuristic approach was better able to efficiently represent and retain the diversity of the entire collection compared with the core identified by clustering approach. Future conservation and breeding efforts will be focused on establishing a separate block in the field gene bank having 49 accessions of cashew core collection.

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PHENOTYPIC EVALUATION OF FIFTEEN GLYCINE MAX (L.) MERRILL (VEGETABLE SOYBEAN) VARIETIES UNDER MINERAL AND BRIS SOILS OF MALAYSIA

Jurnal Teknologi ◽

10.11113/jt.v77.6716 ◽

2015 ◽

Vol 77 (24) ◽

Author(s):

Siti Nurul Farhana Abu Bakar ◽

Ing Chia Phang ◽

Mohd Shukor Nordin ◽

Maizatul Akma Ibrahim

Keyword(s):

Glycine Max ◽

Mineral Soil ◽

The Other ◽

Phenotypic Traits ◽

Vegetable Soybean ◽

Phenotypic Characteristics ◽

Breeding Programs ◽

Glycine Max L ◽

Development Center ◽

Selection Of

Glycine max (L.) Merrill (vegetable soybean) is an important vegetable mainly among the Asian community. It is mainly consumed by human as a highly nutritious and savory snack. Instead of having a relatively higher protein and lower oil contents, it is also has a sweet and better tasting. Thus, this study aims to investigate the phenotypic characteristics of fifteen varieties of Glycine max (L.) Merrill developed by the Asian Vegetable Research and Development Center (AVRDC), Taiwan in order to select the potential varieties to be planted under Malaysian environments. The fifteen varieties were planted under mineral and bris soils at International Islamic University Malaysia (IIUM) Kuantan, Pahang. Eight phenotypic traits included the seed numbers per plant, the pod numbers per plant, the weight of fifteen seeds per plant, the days to emergence per plant, the days to flowering per plant, the plants height per plant, the pods width per plant and the pods length per plant were measured. Selection of potential varieties were mainly done by determining the yielding characteristics. Among these eight morpho-agronomic characteristics, the seed numbers per plant is the main yield determinant while, the other characteristics would be useful for future breeding programs. From the observation, Variety 4 (AGS429) obtained the highest seed numbers per plant (81 seeds) under mineral soil and Variety 1 (AGS 190) produced the highest seed numbers per plant (91 seeds) under bris soil, thus having the promising higher yielding ability to be selected as a potential vegetable soybean varieties to be planted under Malaysian conditions.

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Cowpea [Vigna unguiculata (L.) Walp.] core collection defined by geographical, agronomical and botanical descriptors

Plant Genetic Resources ◽

10.1017/s1479262107837166 ◽

2007 ◽

Vol 5 (03) ◽

pp. 113-119 ◽

Cited By ~ 27

Author(s):

V. Mahalakshmi ◽

Q. Ng ◽

M. Lawson ◽

R. Ortiz

Keyword(s):

Core Collection ◽

International Institute ◽

Pests And Diseases ◽

The Core ◽

Land Race ◽

Drought Tolerant ◽

Selection Processes ◽

World Collection ◽

Entire Collection ◽

The Tropics

Cowpea is a drought-tolerant food legume grown in the savannah regions of the tropics and subtropics. The International Institute for Tropical Agriculture (IITA) holds the world collection of 15,003 cultivated cowpea from 89 countries in its genebank. In excess of 12,000 accessions were characterized for 28 agrobotanical descriptors. The entire collection was first stratified by country of origin and biological status. Land race accessions (10,227) with information on origin and characterization data were grouped using clustering procedures. The clustering analysis was based on Euclidean distances between and among accessions. Accessions within each country were then grouped hierarchically, according to their similarity. The number of clusters selected for countries varied from 2 to 20, depending on the size of collection for that country. A percentage number of accessions (5–25%) was chosen from each country, based on the size of the collection and its proximity to the centre of diversity. The number of accessions from each cluster in a country was then chosen randomly, based on the predetermined percentage. In countries where the numbers of accessions were few ( < 10), the percentage chosen from those countries would be higher and may go up to 100% to ensure that at least one accession was chosen from every country. Accessions with no characterization information were treated as a group, and accessions were chosen randomly, based on their geographical distribution. In the process of selection, 200 accessions that are known to be resistant to pests and diseases and not originally chosen through the selection processes were, nevertheless, kept as part of the core collection. Following these procedures, a total of 1701 accessions of landraces were chosen from the entire collection. Using the same procedures, a subset of 225 accessions was chosen from 1422 advanced cultivars and breeding or research lines. A third subset of 130 accessions was chosen from 838 accessions that either lack information on origin or biological status, and six accessions of wild and weedy forms from the available 64 wild and weed accessions were added. Thus a core collection of 2062 accessions of cowpea was constituted. The diversity in the core collection was similar to that of the entire collection and correlated traits that may be linked were also preserved in the core collection. This core collection of cowpea provides an opportunity for further exploitation of the cowpea germplasm for improvement of this crop.

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Establishing a core collection of foxtail millet to enhance the utilization of germplasm of an underutilized crop

Plant Genetic Resources ◽

10.1017/s1479262108178042 ◽

2008 ◽

Vol 7 (02) ◽

pp. 177-184 ◽

Cited By ~ 40

Author(s):

Hari D. Upadhyaya ◽

R. P. S. Pundir ◽

C. L. L. Gowda ◽

V. Gopal Reddy ◽

S. Singh

Keyword(s):

Core Collection ◽

Diversity Index ◽

Foxtail Millet ◽

Qualitative Traits ◽

The Core ◽

Underutilized Crop ◽

Entire Collection ◽

Breeding Programmes ◽

Precise Assessment ◽

Germplasm Accessions

Foxtail millet (Setaria italica(L.) Beauv.) is one of the ten small millets and is cultivated in 23 countries. The foxtail millet is valued as a crop of short duration, which is good as food, feed and fodder. In general, grain yield levels of foxtail millet are low in comparison with other staple cereals. The greater use of diverse germplasm in breeding is suggested as a means to improve the productivity of this crop. The International Crops Research Institute for the Semi-Arid Tropics genebank is presently holding 1474 cultivated germplasm accessions from 23 countries. To utilize this diversity in research, a core collection (10% of the entire collection) was established using the taxonomic and qualitative traits data. The germplasm accessions were stratified into three taxonomic races (Indica, Maxima and Moharia). Principal coordinate analysis was performed on 12 qualitative traits for each of the biological races, separately that resulted in the formation of 29 clusters. From each cluster, 10% of the accessions were selected to constitute a core collection of 155 accessions. The composition and diversity of the core collection was validated by the χ2-tests of the frequencies of origin, races, subraces and data on qualitative traits. The analysis of the quantitative traits for mean, range, variance, Shannon–Weaver diversity index and phenotypic associations indicated that the diversity from the entire collection was optimally represented in the core collection. The core subset will be evaluated in replicated trials to make a more precise assessment of diversity and further efforts to identify the sources of agronomic and grain nutritional traits for utilization in breeding programmes.

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Construction of the Core Collection of Catalpa fargesii f. duclouxii (Huangxinzimu) Based on Molecular Markers and Phenotypic Traits

Forests ◽

10.3390/f12111518 ◽

2021 ◽

Vol 12 (11) ◽

pp. 1518

Author(s):

Huifen Xue ◽

Xiaochi Yu ◽

Pengyue Fu ◽

Bingyang Liu ◽

Shen Zhang ◽

...

Keyword(s):

Molecular Markers ◽

Core Collection ◽

Snp Markers ◽

Rate Of Change ◽

Phenotypic Traits ◽

Clustering Methods ◽

Single Linkage ◽

Core Collections ◽

The Core ◽

Linkage Method

To promote the conservation and utilization of Catalpa fargesii f. duclouxii (Huangxinzimu) germplasm resources, a total of 252 accessions were used to construct a preliminary core collection according to phenotypic traits and single nucleotide polymorphism (SNP) markers. In this study, 24 phenotypic traits, namely, 9 quantitative traits and 15 qualitative traits, were investigated. The core collection of C. fargesii f. duclouxii (Huangxinzimu) was constructed to remove redundant samples from the collected materials. First, the phenotypic core collection, with a sample proportion of 30, consisting of 24 clones, was constructed according to two genetic distances (Euclidean distance and Mahalanobis), four system clustering methods (the unweighted pair-group average method, Ward’s method, the complete linkage method, and the single linkage method), and three sampling methods (random sampling, deviation sampling, and preferred sampling). The best construction strategies were selected for further comparison. Three core collections (D2C3S3-30, D2C3S3-50, and D2C3S3-70) were constructed according to the optimal construction strategy at three sampling proportions. The core collection D2C3S3-30 with the best parameters was evaluated by using six parameters: the mean difference percentage (MD), variance difference percentage (VD), periodic rate of range (CR), changeable rate of the coefficient of variation (VR), minimum rate of change (CRMIN), and maximum rate of change (CRMAX). Three core collections (M-30, M-50, and M-70) were constructed by molecular markers, and the optimal core collection M-30 was selected by using five parameters, namely, Ho, He, PIC, MAF, and loci. The combination of D2C3S3-30 and M-30 was used to construct the final core collection DM-45, 45 samples representing the complete range of phenotypic and genetic variability. In this study, phenotypic traits combined with molecular markers were used to construct core collections to effectively capture the entire range of trait variation, effectively representing the original germplasm and providing a basis for the conservation and utilization of C. fargesii f. duclouxii (Huangxinzimu).

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Development of self-pollinated maize lines based on the teosinte collection of the N.I. Vavilov institute of plant industry (VIR)

E3S Web of Conferences ◽

10.1051/e3sconf/202126201010 ◽

2021 ◽

Vol 262 ◽

pp. 01010

Author(s):

Safar Appaev ◽

Alan Kagermazov ◽

Azamat Khachidogov ◽

Murat Bizhoev ◽

Eduard Khatefov

Keyword(s):

Genetic Polymorphism ◽

Core Collection ◽

Optimal Time ◽

Phenotypic Traits ◽

Plant Industry ◽

Maize Breeding ◽

Breeding Programs ◽

The Past ◽

Quantitative Properties ◽

Hybrid Maize

The decline in the genetic polymorphism in maize is a cause of concern for many breeders. VIR maize collection represents the world’s maize variety over the past 100 years. The results of the study of maize quantitative properties based on 169 samples from the VIR collection created with the teosinte are shown. KB 595 hybrid, which belongs to the late-season group and is prone to multi-cob was used as a standard. Sowing and evaluation of phenotypic traits were carried out for 2 years in the foothills of Kabardino-Balkaria, in conditions of sufficient soil moisture, in the optimal time. All measurements were carried out on 10 plants with average values of 2 years and an LSD0.05. The results of the research allocated a core collection of 21 samples that promising for hybrid maize breeding and are characterized by significant height and leafiness of the stem, as well as a tendency to form 2 or more cobs on one stem. It has been suggested that the involvement of the selected core collection of 21 samples in thybrid maize breeding programs will significantly expand its genetic polymorphism and increase grain yield in hybrid combinations.

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Evaluation of the USDA National Clonal Pyrus Germplasm Collection for Resistance to Podosphaera leucotricha

HortScience ◽

10.21273/hortsci.41.3.717 ◽

2006 ◽

Vol 41 (3) ◽

pp. 717-720 ◽

Cited By ~ 1

Author(s):

Maryna Serdani ◽

Robert A. Spotts ◽

Jill M. Calabro ◽

Joseph D. Postman ◽

Annie P. Qu

Keyword(s):

Genetic Diversity ◽

Powdery Mildew ◽

Core Collection ◽

Germplasm Collection ◽

Economic Losses ◽

Podosphaera Leucotricha ◽

Breeding Programs ◽

Natural Field ◽

Resistant Cultivars ◽

The Core

Powdery mildew (PM) occurs worldwide and is prevalent on susceptible cultivars wherever pears are grown, causing economic losses due to russeted fruit and an increased need for fungicides. A core subset of the Pyrus germplasm collection at the USDA National Clonal Germplasm Repository in Corvallis, Ore., was evaluated for resistance to Podosphaera leucotricha, the causal agent of PM, using greenhouse and field inoculations of potted trees. The core collection consists of about 200 cultivars and species selections, representing most of the genetic diversity of pears and includes 31 Asian cultivars (ASN), 122 European cultivars (EUR), 9 EUR × ASN hybrids and 46 pear species selections. Three trees of each core accession were grafted on seedling rootstocks. In 2001–02, trees were artificially inoculated in a greenhouse, grown under conditions conducive for PM, and evaluated for symptoms. The same trees were subsequently evaluated for PM symptoms from natural field infections during 2003 and 2004. In the greenhouse, 95% of EUR and 38% of ASN were infected with PM. Average PM incidence (percent of leaves infected) in the greenhouse (8% for ASN and 30% for EUR) was much higher than incidence in the field (2% for ASN and 5% for EUR) during 2003. Symptoms were also more severe in the greenhouse, with 46% of ASN and 83% of EUR with PM symptoms having a mean PM incidence of >10%. In the field, 42% and 22% of EUR and 23% and 13% of ASN were infected with P. leucotricha in 2003 and 2004, respectively. Field infection was very low during both years, with percentage leaves infected in ASN and species selections significantly different from EUR. In the field, 6% of ASN with PM symptoms had a mean PM incidence >10% during both years, while 15% and 2% of EUR accessions with PM symptoms had a mean PM incidence >10% in 2003 and 2004 respectively. These results should be very useful to pear breeding programs to develop improved PM resistant cultivars in the future, by using accessions with consistent low PM ratings.

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