Diversity in Phenotypic Profiles in Landrace Populations of Vietnamese Rice: A Case Study of Agronomic Characters for Conserving Crop Genetic Diversity on Farm

Phenotypic variation of agronomic characters in aromatic rice (Oryza sativa L.) was analyzed in order to elucidate the genetic diversity of the populations of rice landraces. Thirteen populations in Namdinh province, in the Red River Delta of Vietnam, were studied in both of farmers fields and an experimental field. Only small differences were found in agronomic characters among the populations, including populations containing different varieties. Variations among the populations in the frequency distributions of several characters suggested different degrees of diversity among the populations even among populations with the same variety name. The phenotypic profiles of farmers fields were different from those in an experimental field suggesting the environmental differences between them. One variety cultivated in the Myloc district had different phenotypic characters from the other varieties in the Haihau district more clearly in the experimental field. Since the small phenotypic variation in each of farm might be due to the genetic drift and selection by the farmers, on farm conservation of the landraces of rice is considered to be under a force to decrease phenotypic diversity. The present study suggests that the targeting several farms with different phenotypic profiles contribute to the conservation of regional genetic diversity of the landraces of rice.     

Diversity of common bean (Phaseolus vulgaris L.) germplasm from Portugal

Common bean (Phaseolus vulgarisL.) is a traditional crop in Portugal, where farmers growvarieties selected and maintained by themselves. A collection of 88landraces of common bean was evaluated for 17 quantitative andqualitative traits and the biochemical marker phaseolin to displaythe degree of variation of this germplasm. Agronomic data weresubjected to cluster analysis and several groups were identified,with three groups clustering most of the landraces. Regardingphaseolin variation the C and T banding patterns are the mostfrequent ones, so the origin of the Portuguese beans is thus probablythe Andean region of South America. These results give informationabout the origin, diversity and breeding value of the Portuguesegermplasm, that could be useful to widen the genetic base ofcurrently cultivated bean varieties in Europe.     

Characterisation and Variation of Morphological Traits and Storage Proteins in Spanish Emmer Wheat Germplasm (<Emphasis Type="Italic">Triticum Dicoccon</Emphasis>)

Emmer wheat is hulled wheat that was wide cultivated in Spain at the past. Actually, the most of this germplasm is conserved in Germplasm Banks, and only two small populations have been found in Asturias (North of Spain) in a recent collecting mission. In this work, a collection of 31 Spanish emmer lines developed from identical number of accessions of two Germplasm Banks was analysed for morphological spike traits and seed storage protein composition. Up to seven different botanical varieties were detected, which suggest the presence of a wide diversity, although lower than the historically described 10 botanical varieties. At level of seed storage proteins, the lines showed a high diversity, although the new alleles were present with low frequency in materials with scarce agronomic interest for the farmers (var. atratum, var. lagascae or var. pycnurum). This last circumstance could translate in a lost of variability by genetic drift.     

Changes in the diversity and geographic distribution of cultivated millet (Pennisetum glaucum (L.) R. Br.) and sorghum (Sorghum bicolor (L.) Moench) varieties in Niger between 1976 and 2003

Changes in the diversity of landraces in centres of diversity of cultivated plants need to be assessed in order to monitor and conserve agrobioversity—a key-element of sustainable agriculture. This notably applies in tropical areas where factors such as increased populations, climate change and shifts in cropping systems are hypothesized to cause varietal erosion. To assess varietal erosion of staple crops in a country subjected to various anthropogenic and natural environmental changes, we carried out a study based on a comparison of the diversity of pearl millet and sorghum varieties collected in 79 villages spanning the entire cereal-growing zone of Niger over a 26 year period (1976–2003). For these two crops, the number, name and type of varieties according to important traits for farmers were considered at different spatial scales (country, region, village) at the two collection dates. The results confirmed the high diversity of millet and sorghum varieties in Niger. No erosion of varietal diversity was noted on a national scale during the period covered. Some changes were observed but were limited to the geographical distribution of certain varieties. This highlights that farmers’ management can preserve the diversity of millet and sorghum varieties in Niger despite recurrent and severe drought periods and major social changes. It also indicates that rainfed cereal cropping systems in Niger should remain to be based on millet and sorghum, while reinforcing farmers’ seed systems.     

Neglected landraces of collard (Brassica oleracea L. var. viridis) from the Carolinas (USA)

A common garden crop grown in the coastal plain region of North and South Carolina (United States) is the non-heading, leafy green type of Brassica oleracea L. known as collard (B. oleracea L. subsp. oleracea convar. acephala (DC.) Alef. var. viridis L.). Predominantly a fall and winter vegetable in this region, collard is often the only green planting to be found in the yard or garden of a rural home during these cool seasons. Historically, the traditional collard patch and even commercial fields were planted with unique varieties perpetuated by individual seed savers, and collectively, the regional diversity for this crop was probably very significant for well over a century. Genetic erosion of this collard germplasm pool has been severe in recent decades as commercial hybrids have been adopted by both large-scale producers and home gardeners. Although a significant number of collard landraces are being perpetuated to this day, existing diversity among landraces still grown in the region is now in the hands of an aging population of seed savers who maintain germplasm through on-farm preservation. From 2003 to 2006, we explored the coastal plain region of North and South Carolina in search of collard gardens containing traditional landraces. Exploration trips were conducted mid-winter to early spring. About 90 samples of collard were obtained from seed savers during the course of this exploration. Observations of morphological differences of these landraces indicate that significant diversity exists in this group. Obtained landraces are being deposited into the U.S. plant introduction collection and will be available for future use. This preserved collection could prove to be an important new source of genes for B. oleracea improvement.     

Naming of traditional rice varieties by farmers in the Lao PDR

The Lao Ministry of Agriculture and Forestry (MAF)and the International Rice Research Institute (IRRI)jointly collected rice germplasm in the Lao PDR between 1995 and2000. Among the 13192 samples collected, there are 3169 distinctvariety names. Sometimes, the same variety is called by differentnames by different ethnic groups; furthermore clearly differentvarieties have the same name. Lao farmers assign names to traditionalvarieties that relate to the production ecosystem, endosperm type,and maturity. The name also often indicates a variety'sparticular morphological features or other unique characteristics.Varieties are also named for plants, flowers, fruits and animals.Resistance to or tolerance for commonly occurring stress factors likedrought, floods, lodging, birds, weeds and adaptation to soils arealso reflected in some rice variety names. Use of this informationcan help select germplasm for rice improvement.     

The Spanish barley core collection

Spanish barleys constitute a germplasm group of particular interest for breeding purposes, as Spain has been proposed as a possible centre of origin of the crop. The Spanish National Germplasm Bank (Banco Nacional de Germoplasma, BNG), holds a collection of about 2000 barley accessions, mostly landraces collected in Spain prior to extensive introduction of modern varieties. The objective of this work is to create a core collection of barleys representative of old barley genotypes grown in Spain. The core collection will be constituted by three groups of germplasm: successful old varieties (15); entries in common with previously existing barley core collections (15); and 2-row (8) and 6-row (122) entries from the BNG, for a total of 160 entries. Entries were allocated by stratified sampling in agro-ecological uniform zones of barley cultivation in Spain. Classification of agro-ecological regions for barley was based on historical yield records for Spanish provinces. The number of entries for each region was determined in proportion to the logarithm of historical barley acreage. Final choice of accessions within provinces tried to maximize the diversity and avoid duplications by looking at passport data, and to agronomic evaluation data available for a group of about 900 accessions.     

Phenotypic diversity of barley powdery mildew resistance sources

One hundred and twenty-one of 123 previously detected new sources of wild barley (Hordeum vulgare ssp. spontaneum) resistant to powdery mildew (Blumeria graminis f. sp. hordei), and originating from Mediterranean area, and 20 standards were tested at the seedling stage for reaction to 38 selected Israeli powdery mildew isolates. The obtained resistance spectrum (a set of resistant and susceptible reactions) of each accession was divided into triplets and converted to octal numbers. This concentrates information on the resistance phenotype of each accession and makes their comparison much easier. One hundred and thirty-four different resistance spectra were determined. No compatible reaction was found in standards possessing genes mlo and Mlhb2 and in the accession PI 466634. The results demonstrate large diversity in new resistance sources, their distinction from the sources described till now as well as diversity in powdery mildew resistance of wild barley in the Mediterranean area. The results facilitate more effective further studies of such a large set of new resistance sources, and contribute to speeding up their use in barley breeding.     

Marker-assisted optimization of an expert-based strategy for the acquisition of modern lettuce varieties to improve a genebank collection

To regularly improve the composition of the lettuce collection of the Centre for Genetic Resources, the Netherlands (CGN) with modern varieties, feedback from crop experts is used to select approximately 10% of the new material for incorporation in the collection. In the present study, assessments of six experts were compared to microsatellite data of 414 new varieties and 1408 existing accessions. Based on the microsatellite data, the extent to which the genetic diversity of the collection would be enriched (added value) was calculated for specific sets of new varieties. When individual assessments of experts were evaluated, the total added value of expert-based selections was not significantly higher compared to randomly chosen groups, except for a single expert. Unfamiliarity with new varieties was shown to be a crucial factor in the assessment of crop experts. According to the current acquisition protocol that seeks for consensus among experts, varieties are selected based on recommendations from at least three experts. This protocol also did not perform better than randomly chosen groups of new varieties. However, significantly better results were obtained with alternative protocols. It was concluded that breeding value was a more decisive criterion in the current acquisition protocol than maximal extension of the genetic diversity within the collection. A modified protocol addressing both commercial and diversity aspects was suggested in order to meet the demands of plant breeders as well as conservationists.     

Powdery Mildew Resistance in a Collection of Chinese Barley Varieties

One hundred and forty-seven Chinese barley varieties maintained at the Gene Bank of the National Barley Improvement Centre, Zhejiang, and 84 progenies from these varieties were tested at the seedling stage for their reaction to 32 selected pathotypes of Blumeria graminis f. sp. hordei. Eighteen resistance spectra were identified comprising single or combined resistances from eight known (Ml(Bw), Ml(Ch), Mla7, Mla8, Mla9, Mla13, MlaRu4 and Mlg) and six unknown resistance genes. The most frequent gene was Ml(Bw), which was found in 69 varieties and previously detected in only a few European winter barley varieties. The genes Mla8 and Ml(Ch) were also often present, but other resistance genes were rare. After inoculation, considerably fewer pathogen colonies were observed in ‘Aiganqi’ and one line of ‘Tong5’. Twenty varieties were composed of lines with different resistance genes. China is likely to be a region of origin of the genes Ml(Bw), Mla7, as well as three unknown genes found in original landraces and perhaps another three unknown genes detected in cultivars bred in China. The resistances of varieties from the Zhejiang province and those originating from 11 other Chinese provinces were quite different. Unfortunately, none of the varieties are promising sources of resistance to powdery mildew and China does not seem to be a region suitable for identifying such sources.     

A method for establishing a core collection of Saccharum officinarum L. germplasm based on quantitative-morphological data

A technique is proposed for establishing a representative core collection of S. officinarum accessions from the world collection of sugarcane germplasm maintained at the Sugarcane Breeding Institute-Research Centre, Cannanore, India. In the proposed method, the accessions were first sorted based on their relative contributions to the total variability by means of principal component scores based on a set of quantitative characters. Then, the cumulative proportion of their contributions to the total variance was computed. A logistic regression model was fitted to evaluate the functional relationship between the cumulative proportion of variance and the number of accessions. The size of the core set was decided as the inflection point on that fitted curve, i.e., the point beyond which the rate of increase in cumulative proportion of variability contributed by an accession began to decline. A method for eliminating entries with a high degree of similarity from the selected core set is also proposed.     

Phenotypic diversity in the pigeonpea (<Emphasis Type="Italic">Cajanus cajan</Emphasis>) core collection

The pigeonpea core collection developed at ICRISAT genebank consists of 1,290 accessions from 53 countries. The core collection, which includes selected lines in extra early, early, medium and late maturity groups was evaluated for 18 qualitative and 16 quantitative characters during the 2004 rainy season, to assess the phenotypic diversity and determine the relative importance of different characters in evaluating pigeonpea germplasm accessions. The four maturity groups differed significantly for all characters under study. The medium maturity group showed significantly higher mean number of primary, secondary and tertiary branches, number of racemes, pod bearing length, pods per plant, shelling percent and plot seed yield. Late maturity group showed significantly higher mean for leaf size, plant height, pod length, seeds per pod and 100-seed weight, indicating this group as a good source of vegetable pigeonpea. Significant positive correlations were found between number of secondary branches and pods per plant in extra early group (r = 0.756), late maturity group (r = 0.776) and entire core (r = 0.728) and between number of racemes and pods per plant in all maturity groups and entire core. Principal coordinate and principal component analysis showed that seven qualitative and nine quantitative traits were important in explaining multivariate polymorphism. The Shannon–Weaver diversity index (H′) varied for different maturity groups and traits. Phenotypic diversity, averaged over all the 16 characters, increases from extra early group (0.36 ± 0.04) to late maturity group (0.42 ± 0.04) suggesting that medium and late maturity groups have greater diversity compared to extra early and early maturity groups.     

Agronomic traits of exotic barley germplasms resistant to soil-borne mosaic-inducing viruses

Summary In order to obtain information on agronomic performance and potential use of yellow mosaic virus resistant barley germplasms (Hordeum vulgare L.) in breeding programmes, twenty-six varieties were tested for agronomic traits in two years trials. The varieties tested differ in their reaction to the soil-borne mosaic-inducing viruses (BaMMV, BaYMV, BaYMV-2) and their genetic base of BaMMV-resistance. All of the exotic varieties tested are of inferior agronomic performance as compared to resistant German cultivars. Grain yield ranged from 77% to 33% in comparison to the highest yielding German winter barley cultivar Franka. Furthermore, a large variation was also observed in thousand grain weight, number of grains per spike, height, lodging, winterkilling and susceptibility to scald (Rhynchosporium secalis (Oudem) Davis).     

Rice Diversity Collection,Conservation and Management in Northeastern India

Rice is the principal crop of northeastern region of India, where a considerable range of diversity exists. The germplasm collection has also unfold the occurrence of large number of rice landraces in the region. Between 1985 and 2002, a total 2639 accessions of rice germplasms including their wild relatives have been collected. Most of these germplasm material have been conserved in the National Gene Bank, New Delhi following their necessary characterization and evaluation. With the establishment of the Regional Gene Bank Module with medium-term storage facilities (6–7°C with 40–45% relative humidity) at Barapani, Meghalaya, the rice germplasm conservation (ex situ) have been initiated in the region.     

Trade-offs between on-farm varietal diversity and highly client-oriented breeding — a case study of upland rice in India

On-farm varietal diversity is now highest in marginal agricultural environments because, unlike the case in more favourable areas, modern varieties have not been a sufficiently attractive option for farmers to replace their landraces. However, the continued survival of landraces on farm is dependent on the continuing failure of plant breeding to provide better alternatives. Highly client-oriented breeding can produce suitable modern varieties for areas that were dominated by landraces. We examine here the case of the adoption of two upland rice varieties in three states in eastern India, Jharkhand, West Bengal and Orissa, where our surveys had confirmed low adoption of modern varieties in the upland ecosystem. The two new upland varieties were readily accepted by farmers who rapidly adopted them on large proportions of their land. On-farm diversity is maintained by the need to trade-off among varieties but once a variety with overall superiority was found this incentive was removed. The new varieties from the client-oriented breeding did not have weaknesses that farmers had to trade-off against their landraces so they were more likely to replace them. They also replaced older modern varieties. Farmers had previously maintained them along with landraces because they had to trade-off the higher yield of Kalinga III against the more stable yield of landraces or the higher yield of Vandana against the higher gain quality of the landraces. Only mean count per household could be used to test the significance of the differences between individual years. In all states, this revealed a significant reduction in landrace diversity with the adopting farmers when the addition of the two new varieties was not considered. Trends across years for mean varietal count, total count and Shannon–Wiener index showed a significant decline in Orissa, irrespective of whether the two new varieties were included in the analysis or not. In Jharkhand there was a significant decline only for mean count when the new varieties were not included. In Orissa, it was possible to test if rare landraces were as readily replaced as more common ones. Landrace replacement was unmitigated by increasing rarity yet the most rare landraces have the highest priority for genetic conservation. Some landraces were completely replaced by the farmers in the sample despite a diverse variety portfolio being a risk-reducing strategy in a region where there is a high risk of crop failure. There was little environmental heterogeneity in the marginal, drought-prone areas to slow this decline. The new varieties had an impact on the farming system because sometimes farmers brought additional upland into cultivation. They also introduced these varieties into more favourable, medium land. The strategy of releasing two new upland varieties met with some success in maintaining diversity.     

Patterns of Phenotypic Variation in a Germplasm Collection of Carthamus tinctorius L. from the Middle East

Phenotypic diversity was assessed for quantitative and qualitative traits in a salt-tolerant subset of the international safflower (Carthamus tinctorius L.) germplasm collection originating from 11 countries in three regions (Central Asia, Southwest Asia and Africa) of the Middle East. Phenotypically, the germplasm, among and within regions, was highly variable, especially for rosette- and yield-related traits. Frequency of desirable variants of seven agronomically important traits ranged from 14% for long rosette period to 50% for no or few spines. Level of population differentiation was high for number of capitula per plant (30%), whereas most traits partitioned their diversity (82–87%) within populations. Region-specific nonrandom associations among sets of qualitative traits and the existence of broad morphological and phenotypic diversity in this germplasm were supported by the large number of log-linear models needed to describe qualitative trait associations, the high number of principal components needed to account for total variability, and the low discriminatory power of phenotypic traits among germplasm from regions and countries in the Middle East. These results suggest that adaptation of the species to the wide spatial and temporal variation in the Middle East resulted in a multitude of ecotypes and in enormous amount of local variation. A multivariate selection criterion for high biological and seed yield, long rosette period and no or few spines identified five accessions from Southwest Asia that can be introduced into subsistence farming systems as a multipurpose crop under saline agriculture.     

Marker-Assisted Acquisition and Core Collection Formation: A Case Study in Barley using AFLPs and Pedigree Data

A problem that often occurs in deciding which germplasm should be acquired to expand the diversity of a plant genetic resources collection, and which accessions should be included in a core collection, is the lack of proper data. The usefulness of an AFLP-based protocol to assist in acquisition decisions and in core collection formation was examined by using 52 barley cultivars. For validation purposes, pedigree data of the cultivars were used to calculate the ‘effective number of origin lines’ (n_o1), a parameter introduced in earlier research that was defined as the number of alleles per locus, not identical by descent, in a set of lines. Two AFLP primer combinations were able to distinguish all 52 cultivars from each other, and to discriminate between spring and winter crop types. Using the year of origin of the cultivars, the historical development of n_o1 showed a stepwise pattern, indicating the periodical release of genetically similar cultivars, alternated by the incorporation of new material. Comparison of AFLP data between cultivars and both their parents was possible in five cases. These comparisons revealed a high likelihood that the correct parents were involved but a rather skewed contribution of parents to offspring, suggesting that backcrossing had been applied. Treating the 25 cultivars that were released before 1980 and played an important role in barley cultivation as a basic collection, and the 27 more recent cultivars as potential candidates for acquisition, n_o1 values generated by a marker-based approach largely followed those using a random approach. Given this poor performance, a marker-based protocol to assist in acquisition decisions was not considered useful for the analysed material. If the 52 cultivars were considered to be the collection from which a core collection had to be selected, the marker-based selection showed much better results compared to a random selection. About half of the total number of origin lines could be captured with a quarter of the collection, indicating the potential utility of AFLPs in core collection formation.     

Variation of Agro-morphological Characters in Moroccan Barley Landraces Under Near Optimal and Drought Conditions

In many areas of North Africa, barley is often the only possible rainfed crop. In these regions water deficit is the primary constraint affecting crop production. Twenty barley landraces collected from different localities in south Morocco and four modern varieties were characterized in two field experiments, one under well-irrigated and one under limited-irrigated conditions. Nine agro-morphological characters were evaluated: Plant height, tiller number per plant, number of grains per spike, number of spikes per plant, spike weight, spike length, plant weight (PW), number of internodes of rachis (NIR), and length of the last internode of rachis. The correlation coefficients among characters were nearly the same in the well- and limited-irrigated experiment. Under limited-irrigated conditions, plant growth was significantly decreased as measured by all characters except NIR, which was unaffected. The percentage of reduction, ranging from 80.08% to 5.82%, was recorded on PW and NIR, respectively. The injury index ranging from 4.02 to 0.06 was recorded on PW and NIR, respectively. Using discriminant analysis the genotypes were arranged in three, clearly separated groups that varied in their tolerance to drought stress.