‘Sikkim Primitive’ (SP) maize locally known as ‘murali makkai’ in Sikkim is a unique genetic resource exhibiting prolificacy and excellent popping capacity. Status of SP has reached extinction level due to its very small population size and neglected conservation efforts in-situ. In an initial effort to conserve and revive this landrace, characterization and documentation was carried out with 31 morphologically assayed traits recorded at different growth stages along with molecular characterization with simple-sequence repeat (SSR) markers. Plants exhibited prolificacy (5–6 cobs/plant) and excellent popping capacity along with other distinct traits. Plants were tall with thin stem, loose drooping tassel with anthocyanin coloration present at the base of glumes and in brace roots. Cobs were medium sized carrying small seeds with low test weight (87.90 g). A total of 22 SSR markers show amplification in murali makkai with markers bnlg1083, umc1353, umc1128, bnlg1017, bnlg2077, umc2298 and umc2373 amplified unique amplicons ranging from 100 to 800 bp. The characterized set of traits and molecular characterization for murali makkai will facilitate in utilization for genetic improvement and maintenance of genetic purity.

White Guinea yam (Dioscorea rotundata Poir.) is indigenous to West Africa, a region that harbours the crop's tremendous landrace diversity. The knowledge and understanding of local cultivars’ genetic diversity are essential for properly managing genetic resources, conservation, sustainable use and their improvement through breeding. This study aimed to dissect phenotypic and molecular diversity of white yam cultivars from Benin using agro-morphological and single nucleotide polymorphism (SNP) markers. Eighty-eight Beninese white Guinea yam cultivars collected through a countrywide ethnobotanical survey were phenotyped with 53 traits and genotyped with 9725 DArT-SNP. Multivariate analysis using phenotypic traits revealed 30 traits as most discriminative and explained up to 80.78% of cultivars’ phenotypic variation. Assessment of diversity indices such as Shannon–Wiener (H′), inverse Shannon (H.B.), Simpson's (λ) index and Pilou evenness (J) based molecular and phenotypic data depicted a moderate genetic diversity in Beninese white Guinea yam cultivars. Genetic differentiation of cultivars among country production zones was low due to the high exchange of planting materials among farmers of different regions. However, there was high genetic diversity within regions. Hierarchical clusters (HCs) on phenotypic data revealed the presence of two groups while HCs based on the SNP markers and the combined analysis identified three genetic groups. Our result provided valuable insights into the Beninese white Guinea yam diversity for its proper conservation and improvement through breeding.

In order to understand rice blast resistance gene patterns in rice landraces from Myanmar and Laos, we analysed the Pita, Pib, Pikh, Pi9 and Pi5 genes in 80 landraces through the use of functional molecular markers and functional fragment sequencing. These landraces were separated into four haplotypes (H1–H4) based upon three mutations identified in the Pita sequence. All four haplotypes were detected among landraces from Myanmar, whereas only the H1 and H2 haplotypes were detected among landraces from Laos. We additionally grouped landraces carrying 0–4 resistance genes into 18 genotypes based upon their resistance-susceptibility patterns and found that 16 of these genotypes were detected among Myanmar landraces at relative frequencies ranging from 2.50–12.50%, while 10 were detected among landraces from Laos at relative frequencies of 2.50–42.50%. The ‘Pib( + ) pikh(−) pi9(−) pi5(−) pita(−)’ genotype was found to be dominant, accounting for 12.5 and 42.5% of landraces from Myanmar and Laos, respectively. The Pib, Pikh, Pi5 and Pita genes were detected in 52.50, 32.50, 37.50 and 30.00% of landraces from Myanmar respectively, whereas they were detected in 52.50, 12.50, 30.00 and 17.50% of landraces from Laos, respectively. The Pi9 gene was rarely detected among analysed landraces and was particularly rare in those from Laos. These findings suggest that rice landraces from Myanmar are more genetically diverse than those from Laos, with clear differences in blast resistance gene patterns between landraces from these two countries.

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating fungal disease of wheat (Triticum aestivum L.). The best economical technique for disease control is breeding for genetic resistance to stripe rust. To find resistance genes in landrace PI388222 from Pakistan, a segregating population was developed by a cross between PI388222 and susceptible Australian spring wheat line Avocet ‘S’. The F2:4 seeds were harvested and seeds were planted in the greenhouse of Washington State University Pullman, to grow F4:5 recombinant inbred lines (RIL). A variable set of seedling reactions were noted when a set of 136 F5 and parental lines were screened with four Puccinia striiformis f. sp. tritici races (PSTv-37, PSTv-40, PSTv-4 and PSTv-51). The great proportion of RILs showed resistant reaction displayed by the RILs was against PSTv-40, for which 85% of the RILs showed resistant reaction, while less resistance to the race PSTv-37 was detected against which the resistance was for only 49% of the RILs. The RIL population was further evaluated at two locations; Palouse Conservation Field Station (PCFS) and Mount Vernon (MV). In MV field, 76% of RILs displayed resistant reaction while 15% of RILs exhibited moderate reaction. About 53% of RILs exhibited resistant reaction to four P. tritici races that were used in glasshouse screening and they were also resistant in field environments at PCFS and MV. This study demonstrates that landrace comprises partial resistance in the range of resistant to moderately resistant lines.

In this work, 10 processing type Hungarian tomato gene bank accessions were investigated in a 3-year open-field experiment together with three commercial varieties for quantifying the genotype × environment interaction for their total soluble solids, total acid, dry matter, lycopene, total polyphenol content and antioxidant activity. Results showed remarkable differences of accessions in phytonutrient content over the 3 years (environments). Genotype main effect plus genotype × environment interaction biplots were created for the visualization of the best performing samples and of their relation to a theoretical best variety. Obovate fruit-shaped accessions (especially RCAT031257 and RCAT060349) reached outstanding nutritional results in every environment. According to extremities in weather conditions, two landraces (RCAT060348 and RCAT060349) with higher drought tolerance, and two (RCAT031257 and RCAT029837) less prone to excessive rainfalls were identified. The results can contribute to the enrichment of tomato nutritional phenotypic data banks, facilitating the utilization of gene bank accessions in genomic studies.

Landraces (including heritage varieties) are an important agrobiodiversity resource offering considerable value as a buffer against crop failures, as a crop for niche markets, and as a source of diversity for crop genetic improvement activities underpinning future food security. Home gardens are reservoirs of landrace diversity, but some of the accessions held in them are vulnerable or threatened with extinction. Those associated with seed saving networks have added security, for example, ca. 800 varieties are stored in the Heritage Seed Library (HSL) of Garden Organic, UK. In this study, Amplified Fragment Length Polymorphisms-based genetic analysis of accessions held in the HSL was used to (a) demonstrate the range of diversity in the collection, (b) characterize accessions to aid collection management and (c) promote broader use of the collection. In total, 171 accessions were included from six crops: Vicia faba L., Pisum sativum L., Daucus carota L., Cucumis sativus L., Lactuca sativa L. and Brassica oleracea L. var. acephala (DC.) Metzq. Average expected heterozygosity ranged from 0.18 to 0.28 in D. carota; 0.02–0.18 in P. sativum; 0.05–0.18 in L. sativa; 0.15–0.26 in B. oleracea var. acephala; 0.15–0.37 in C. sativus and 0.07–0.36 in V. faba. Genetic diversity and Fst values generally reflected the breeding system and cultivation history of the different crops. Comparisons of the diversity found in heritage varieties with that found in commercial varieties did not show a consistent pattern. Principal coordinates analysis and Unweighted Pair Group Method with Arithmetic Mean cluster analysis were used to identify four potential duplicate accession pairs.

This study was conducted to characterize new plant type (NPT) traits among 650 genetically diverse rice genotypes of tropical japonica and indica and to establish an initial core set for NPT traits. Analysis of variance revealed highly significant differences among the genotypes for all the traits assessed except flag length and width and leaf angles. Dendrogram categorized the genotypes into five distinct duration groups. Genotypes viz., Pumphamah, IRGC5097, IRGC37015, IRGC43741, IRGC50448, IRGC53089, IRGC39111, IRGC18021, Haorei Machang, IRGC44069, IRGC8269, Thangmoi, IRGC33130 and IRGC29772 were identified as possessing strong culm. Long panicles with a length of more than 35 cm were found in IRGC8269, IRGC9147, IRGC14694, IRGC19642, IRGC27435, IRGC39111, IRGC31051, IRGC26011and IRGC25892. Ideal leaf angle of NPT genotypes of 5°, 10° and 20° of flag leaf, 1st and 2nd leaves was not found in any genotype but with a combination of 5°, 10° and 10° was observed in IRGC63102 and IRGC66644. NPT flag leaf length and width of 50 and 2 cm, respectively, was seen in ‘Kemenya Kepeu’ and ‘IRGC29772’. High grain number of more than 350 was observed in IRGC53089, IRGC31063 and Azhoghi. A total of 72 genotypes were found with a combination of one or more ideal plant type traits of which, hierarchical cluster analysis based on genetic distances selected 32 as NPT core set. This core set will serve as an ideal genetic resource for breeding programs aimed at NPT development.

A total of 326 pearl millet accessions selected for fodder traits from the world collection at ICRISAT genebank, India were evaluated in rainy, postrainy and summer seasons to identify promising sources for fodder yield. In rainy season, majority of accessions grew significantly tall, produced thick stems, long and broad leaves compared with postrainy and summer seasons. Total tillers per plant were significantly more in rainy and summer seasons than in postrainy season. Significant (P = 0.05) positive correlations were observed among all traits in all seasons except total tillers, which showed significant negative correlation with all other traits but for a few cases. Accessions of cluster 1 flowered early and produced more tillers per plant, while those of cluster 3 flowered late, grew tall, produced thick stems, more leaves per plant, which were long and broad. Promising sources identified include IP 11839 and IP 11840 for plant height and number of leaves per plant, IP 15710, IP 15735 and IP 15752 for stem thickness and leaf width, and IP 3628, IP 15285, IP 15288, IP 15302, IP 15342, IP 15351, IP 15290, IP 20347 and IP 20350 for total tillers per plant. Further testing of these sources of fodder traits at different locations will be very useful.

In many regions of the world, the cultivation of landraces is still common, in particular in centres of crop diversity. Significant effort has been put into ex situ conservation of landraces but limited data exist on the changes in genetic diversity that occur over time in farmers’ fields. We assessed temporal changes in barley landrace diversity in Jordan using seed samples collected in 1981 and 2012 from the same locations. We did not observe significant changes in the amount of genetic diversity, but samples collected in 2012 were more homogenous and less locally distinct. In two sites, we observed replacement of the old material. We observed a change in phenotype, and phenotypes were found to be more homogeneous among sites in 2012. Climate changed significantly over the study period, becoming hotter and dryer, but we did not identify any correlation between the changes in climate and genetic and phenotypic variations. While the amount of genetic diversity in terms of allelic richness and number of multi-locus genotypes has been maintained, local distinctiveness among landrace barley populations in Jordan was reduced.

The genebank at ICRISAT, India that serves as a world repository for sorghum germplasm conserves 39,234 accessions from 93 countries, including 6249 from seven South Asian countries: Afghanistan (6), Bangladesh (9), India (6101), the Maldives (10), Nepal (8), Pakistan (90) and Sri Lanka (25). A total of 5340 georeferenced accessions were used to identify gaps, and 5322 accessions that were characterized at ICRISAT were used to assess the diversity in the collection. Accessions of basic races varied widely than those of intermediate races for flowering in the postrainy season, plant height in both rainy and postrainy seasons, panicle exsertion, panicle length and width, seed size and 100 seed weight. Landraces from India were late flowering, tall and produced stout panicles and larger seeds. Landraces from Pakistan flowered early in both seasons and produced stout panicles and those from Sri Lanka were late flowering and tall in both seasons, produced more basal tillers and stout panicles. A total of 110 districts in 20 provinces of India, 13 districts in three provinces of Pakistan, three districts in Bangladesh and five districts in four provinces of Sri Lanka were identified as geographical gaps. Sorghum bicolor subsp. verticilliflorum, S. halepense and S. propinquum were identified as taxonomic gaps in the collection. Therefore, it is suggested to explore the districts identified as gaps to enrich the variability in the world collection of sorghum at ICRISAT.

The world collection of pearl millet at ICRISAT genebank includes 19,696 landraces. Passport and characterization data of 2,929 accessions belonging to 89 named landraces originating in 15 countries of Africa was used to study the adoption pattern and genetic potential. Out of 89 named landraces under study, 71 were grown in one country, 11 in two countries, six in three countries and one in four countries. Latitude and prevailing climate at collection sites were found as the important determinants of cultivation pattern of landraces. A hierarchical cluster analysis using 12 agronomic traits resulted in five clusters. Cluster 1 for late flowering, short height in rainy season, high tillering and thin panicles; cluster 2 for early flowering; cluster 3 for stout panicles in both the seasons and larger seeds and cluster 5 for longer panicles in both seasons, were found as promising sources. IP 8957, IP 8958, IP 8964 of Iniadi landrace for short height, downy mildew and rust resistance and high seed iron and zinc contents; IP 17521 of Gnali (106.9 ppm) and IP 11523 of Idiyouwe (106.5 ppm) for high seed iron content; IP 17518 of Gnali (79.1 ppm) and IP 11535 of Iniadi (78.4 ppm) for high seed zinc content were the important sources. All accessions of Raa for high seed protein content (>15%) and those of Enele for drought tolerance, were found to be promising sources. Further evaluation of promising sources identified in this study is needed for enhanced utilization of germplasm in pearl millet improvement.

This is the first report on increasing yield and nutritional content of snake melon (Cucumis melo L. var. flexuosus) by exploiting intraspecific genetic variation of genetically diverse melons. Inbred snake melon ‘Punjab Long melon 1’ (PLM1) was hybridized with five genetically diverse inbred melons: KP 7 (var. momordica), AM 72 (var. acidulus), ‘Arya 1’ (var. chate), 04-02 (var. tibish) and ‘Punjab Wanga’ (unknown botanical variety). The parents and hybrids were evaluated at three locations for nine traits. Hybrids PLM1 × 04-02 and PLM1 × ‘Punjab Wanga’ exhibited significant (P0.05) heterosis for the number of marketable fruits per plant, and ascorbic acid and carotenoid contents of marketable fruits.

Season-long monitoring of on-farm rice (Oryza sativa, L.) plots in Nepal explored farmers' decision-making process on the deployment of varieties to agroecosystems, application of production inputs to varieties, agronomic practices and relationship between economic return and area planted per variety. Farmers deploy varieties [landraces (LRs) and modern varieties (MVs)] to agroecosystems based on their understanding of characteristics of varieties and agroecosystems, and the interaction between them. In marginal growing conditions, LRs can compete with MVs. Within an agroecosystem, economic return and area planted to varieties have positive relationship, but this is not so between agroecosystems. LRs are very diverse on agronomic and economic traits; therefore, they cannot be rejected a priori as inferior materials without proper evaluation. LRs have to be evaluated for useful traits and utilized in breeding programmes to generate farmer-preferred materials for marginal environments and for their conservation on-farm.

The present study was aimed to compare the developmental changes of carcass composition, meat quality characteristics and organ weight in pigs of different breeds. Six pigs (sex balance) of each breed were slaughtered at 35, 80 and 125 days of age, respectively. The carcass was chilled and the left carcass side was dissected into bone, lean meat, fat and skin; additionally, organ weight and meat quality parameters were observed. Carcasses of the Jinhua pig were lighter (P < 0.001), contained less lean meat percentage (P < 0.01) and more carcass fat percentage (P < 0.05) than did carcasses of the Landrace. L*-values were lower in Jinhua pigs than in Landrace at 125 days of age (P < 0.05), but the Jinhua pig had higher a*-values compared with Landrace at the age of 80 days (P < 0.01) and 125 days (P < 0.01), respectively. In addition, Jinhua pigs showed lower colour scores (P < 0.05), higher intramuscular fat (IMF) percentage (P < 0.05), less marbling scores (P < 0.05) and lower drip loss (P < 0.05) than Landrace. For organ weight, Jinhua pigs had higher relative heart weight at the age of 80 days (P < 0.05) and 125 days (P < 0.001), and higher relative liver weight at 125 days of age (P < 0.01) than that of Landrace. In addition, the relative kidney weight was heavier (P < 0.001) in the Jinhua pig than in the Landrace during the whole experiment. These results indicated that developmental changes of carcass composition, meat quality parameters and organ weight displayed breed differences. Jinhua pigs were fatter than Landrace but the former had better quality characteristics in the meat.

Organic and low-input farmers often plant seed varieties that have been selected under conventional practices, traditionally including high inputs of artificial fertilizers, crop protection chemicals and/or water. In addition, these crops are often selected in environments that may or may not represent the local environment of the farmer. An evolutionary participatory breeding (EPB) method emphasizes the utilization of natural selection in combination with site-specific farmer selection in early segregating generations of a heterogeneous crop population. EPB is a combination of two specific breeding methods, evolutionary breeding and participatory plant breeding. Evolutionary breeding has been shown to increase yield, disease resistance, genetic diversity and adaptability of a crop population over time. It is based on a mass selection technique used by farmers for over 10,000 years of crop improvement. Participatory plant breeding programs originated in developing countries to meet the needs of low-input, small-scale farmers in marginal environments who were often overlooked by conventional crop breeders. The EPB method is an efficient breeding system uniquely suited to improving crop varieties for the low-input and organic farmer. The EPB method utilizes the skills and knowledge of both breeders and farmers to develop heterogeneous landrace populations, and is an effective breeding method for both traditional and modern farmers throughout the world.

Cleveland et al. (2005, Environ. Biosafety Res.4: 197–208) offer useful suggestions for monitoring transgenes in landraces of maize, but we disagree with their statement that the scientific conclusions of our paper (Ortiz-García et al., 2005, Proc. Natl. Acad. Sci. USA102: 12338–12343) are not justified. First, contrary to their perception, our survey was not designed to evaluate transgenes in the whole State of Oaxaca, but rather to monitor a specific portion of the District of Ixtlán de Juárez where the presence of transgenes had been reported previously by Quist and Chapela (2001, Nature414: 541–543). Second, our paper described two methods for estimating frequencies of undetected transgenic seeds, while Cleveland et al. recommend a third approach that explicitly estimates effective population size. They argue that the effective population size of our seed samples is smaller than we assumed, leading to false claims about our detection accuracy. However, we employed a robust statistical approach to compensate for possible bias by using numbers of maternal plants, in addition to numbers of seeds, to provide a conservative estimate of the minimum number of independent samples. When we re-analyzed our 2004 data using effective population sizes, our conclusion that transgenic seeds were “absent or extremely rare” did not change, nor did the general range of possible frequencies of undetected transgenic seeds. Unlike Cleveland et al., we advocate using combined probability tests to analyze data across localities. Third, our critics argue that we accepted the null hypothesis that transgenes were absent. Actually, we assumed that transgenes were present in local landraces, and we used parameter estimation methods to calculate the probability of failing to detect transgenic individuals at a range of frequencies. In agreement with Cleveland et al., we reiterate that there is a clear need for additional surveys with rigorous sampling methods to provide estimates of transgene frequencies over broad geographic areas in Mexico.