Landrace Populations Research Articles

KINERJA JATI ASAL MUNA PADA PLOT UJI KLON JATI DI EMPAT LOKASI

The research was conducted to evaluate the growth of teak clone ( Tectona grandis L.f.) taken from land race population at Muna Island in South East Sulawesi. The trials were planted in 2002 – 2005 in 4 locations as follows: Kemampo (South Sumatera), Kotabaru (South Kalimantan), Gunung Kidul (Yogyakarta) and Wonogiri (Central Java). The growth of teak clones from Muna at 5 years old in 4 locations was as followed: the average of total height (9,98 m, 13,11 m, 7,46 m and 9,37m), diameter/DBH (11,09 cm, 12,80 cm, 7,87 cm and 13,24 cm) and tree volume estimation (0,0624 m3, 0,117 m3, 0,028 m3 and 0,099 m3). The growth performances of teak clone from Muna were stable at middle position in all locations. The best growth was gained in Kotabaru and the lowest in in Gunung Kidul. Keywords : Clonal Test, Muna teak, Tectona grandis L.f.

Genetic characterization of Turkish cultivated emmer wheat [Triticum turgidumL. ssp.dicoccon(Schrank) Thell.] landraces based on isoenzyme analysis

Nineteen landrace populations of Turkish cultivated emmer wheat [Triticum turgidum L. ssp. dicoccon (Schrank) Thell.] were characterized in terms of three isoenzyme [Endopeptidase-1, Aminopeptidase-1 and Aminopeptidase-2] systems, by isoelectric focusing gel electrophoresis. For overall loci, the mean number of alleles and effective alleles were observed as 2.00 and 1.37, respectively. The mean value of gene diversity and average gene diversity, in overall loci, were detected as 0.23 and 0.07, respectively. Actual genetic differentiation and gene flow between different populations were calculated as 0.19 and 0.11, respectively. Pearson's correlation and multiple regression analyses indicated that eco-geographical variables have significant effects on isoenzyme genetic diversity. Landraces that have desirable agronomical and immunological resistance traits that makes them adaptable to climate change and different eco-geographical conditions are important genetic resources to utilise for the improvement of future crops of modern wheat varieties. There is a need to assess the genetic structure and genetic composition of important agronomical characters and to determine the magnitude of the genetic diversity currently conserved in the germplasm of landraces, both in farm fields and in ex situ collections and finally, strategies for the effective use of landraces, particularly of emmer wheat, should be planned and implemented in Turkey were discussed.

Citrullus lanatus germplasm of southern Africa.

Citrullus lanatus germplasm from southern Africa is a rich source of diversity for cultivated watermelon. Wild, feral, and landrace populations of the species are found throughout the arid regions of southern Africa, where they serve as sources of water and food for humans and wildlife alike. Genetic resources from the region proved to be important sources of disease resistance for cultivated watermelon, contributing to the development of both Fusarium wilt- and anthracnose-resistant cultivars. Basic research, such as genomic mapping and the elucidation of drought tolerance, have also benefitted from the abundant genetic diversity. Currently, several ex situ collections in the region and the rest of the world house accessions originating from southern Africa. The USDA germplasm collection has been screened extensively for traits of interest in watermelon breeding, but full advantage has not been taken of some of the other collections. The C. lanatus germplasm from southern Africa is currently a largely un...

Genetic parameter estimation in seedstock Swine population for growth performances.

The objective of this study was to estimate genetic parameters that are to be used for across-herd genetic evaluations of seed stock pigs at GGP level. Performance data with pedigree information collected from swine breeder farms in Korea were provided by Korea Animal Improvement Association (AIAK). Performance data were composed of final body weights at test days and ultrasound measures of back fat thickness (BF), rib eye area (EMA) and retail cut percentage (RCP). Breeds of swine tested were Landrace, Yorkshire and Duroc. Days to 90 kg body weight (DAYS90) were estimated with linear function of age and ADG calculated from body weights at test days. Ultrasound measures were taken with A-mode ultrasound scanners by trained technicians. Number of performance records after censoring outliers and keeping records pigs only born from year 2000 were of 78,068 Duroc pigs, 101,821 Landrace pigs and 281,421 Yorkshire pigs. Models included contemporary groups defined by the same herd and the same seasons of births of the same year, which was regarded as fixed along with the effect of sex for all traits and body weight at test day as a linear covariate for ultrasound measures. REML estimation was processed with REMLF90 program. Heritability estimates were 0.40, 0.32, 0.21 0.39 for DAYS90, ADG, BF, EMA, RCP, respectively for Duroc population. Respective heritability estimates for Landrace population were 0.43, 0.41, 0.22, and 0.43 and for Yorkshire population were 0.36, 0.38, 0.22, and 0.42. Genetic correlation coefficients of DAYS90 with BF, EMA, or RCP were estimated to be 0.00 to 0.09, −0.15 to −0.25, 0.22 to 0.28, respectively for three breeds populations. Genetic correlation coefficients estimated between BF and EMA was −0.33 to −0.39. Genetic correlation coefficient estimated between BF and RCP was high and negative (−0.78 to −0.85) but the environmental correlation coefficients between these two traits was medium and negative (near −0.35), which describes a highly correlated genetic response to selection on one or the other of these traits. Genetic Trends of all three breeds tend to be towards bigger EMA or greater RCP and shorter DAYS90 especially from generations born after year 2000.

Diversity and abundance of the abnormal chromosome 10 meiotic drive complex in Zea mays

Maize Abnormal chromosome 10 (Ab10) contains a classic meiotic drive system that exploits the asymmetry of meiosis to preferentially transmit itself and other chromosomes containing specialized heterochromatic regions called knobs. The structure and diversity of the Ab10 meiotic drive haplotype is poorly understood. We developed a bacterial artificial chromosome (BAC) library from an Ab10 line and used the data to develop sequence-based markers, focusing on the proximal portion of the haplotype that shows partial homology to normal chromosome 10. These molecular and additional cytological data demonstrate that two previously identified Ab10 variants (Ab10-I and Ab10-II) share a common origin. Dominant PCR markers were used with fluorescence in situ hybridization to assay 160 diverse teosinte and maize landrace populations from across the Americas, resulting in the identification of a previously unknown but prevalent form of Ab10 (Ab10-III). We find that Ab10 occurs in at least 75% of teosinte populations at a mean frequency of 15%. Ab10 was also found in 13% of the maize landraces, but does not appear to be fixed in any wild or cultivated population. Quantitative analyses suggest that the abundance and distribution of Ab10 is governed by a complex combination of intrinsic fitness effects as well as extrinsic environmental variability.

Effect of bio and chemical fertilizers on seed yield and its components of dill (Anethum graveolens)

To study the effects of bio and chemical fertilizers on seed yield and some of the yield components of dill (Anethum graveolens L.), a pot experiment was performed at the Research Station of Faculty of Agriculture, Islamic Azad University, Tabriz Branch, Iran, in 2010. This experiment was conducted factorially based on completely randomized design with three replications. Studied factors consisted of dill landrace populations (Mobarakeh Esfahan and Hamadan), mycorrhiza strains (Glomus interadices and Glomus mosseae and a non-inoculated one as control), nitrogen fixing biofertilizers (nitroxin, super nitro plus and a non-inoculated one as control) and chemical fertilizers containing nitrogen in urea form and phosphorus in triple super phosphate form (0, 50 and 100% of the recommended dose). Studied traits were number of umbels and seeds per plant, 1000 seed weight and seed yield. The results showed that mycorrhiza application increased the number of seeds per plant and seed yield nearly 32 and 32.5% more than control, respectively. Application of nitrogen fixing biofertilizers also influenced all characteristics studied, significantly. All the characteristics under study except 1000 seed weight were affected by chemical fertilizers. In addition, results revealed that interaction of factors had significant effect on more of the traits under study.

Twentieth-century changes in the genetic composition of Swedish field pea metapopulations.

Landrace crops are formed by local adaptation, genetic drift and gene flow through seed exchange. In reverse, the study of genetic structure between landrace populations can reveal the effects of these forces over time. We present here the analysis of genetic diversity in 40 Swedish field pea (Pisum sativum L.) populations, either available as historical seed samples from the late nineteenth century or as extant gene bank accessions assembled in the late twentieth century. The historical material shows constant high levels of within-population diversity, whereas the extant accessions show varying, and overall lower, levels of within-population diversity. Structure and principal component analysis cluster most accessions, both extant and historical, in groups after geographical origin. County-wise analyses of the accessions show that the genetic diversity of the historical accessions is largely overlapping. In contrast, most extant accessions show signs of genetic drift. They harbor a subset of the alleles found in the historical accessions and are more differentiated from each other. These results reflect how, historically present metapopulations have been preserved during the twentieth century, although as genetically isolated populations.

Waxy phenotype evolution in the allotetraploid cereal broomcorn millet: mutations at the GBSSI locus in their functional and phylogenetic context.

Waxy mutants, in which endosperm starch contains ∼100% amylopectin rather than the wild-type composition of ∼70% amylopectin and ∼30% amylose, occur in many domesticated cereals. The cultivation of waxy varieties is concentrated in east Asia, where there is a culinary preference for glutinous-textured foods that may have developed from ancient food processing traditions. The waxy phenotype results from mutations in the GBSSI gene, which catalyzes amylose synthesis. Broomcorn or proso millet (Panicum miliaceum L.) is one of the world’s oldest cultivated cereals, which spread across Eurasia early in prehistory. Recent phylogeographic analysis has shown strong genetic structuring that likely reflects ancient expansion patterns. Broomcorn millet is highly unusual in being an allotetraploid cereal with fully waxy varieties. Previous work characterized two homeologous GBSSI loci, with multiple alleles at each, but could not determine whether both loci contributed to GBSSI function. We first tested the relative contribution of the two GBSSI loci to amylose synthesis and second tested the association between GBSSI alleles and phylogeographic structure inferred from simple sequence repeats (SSRs). We evaluated the phenotype of all known GBSSI genotypes in broomcorn millet by assaying starch composition and protein function. The results showed that the GBSSI-S locus is the major locus controlling endosperm amylose content, and the GBSSI-L locus has strongly reduced synthesis capacity. We genotyped 178 individuals from landraces from across Eurasia for the 2 GBSSI and 16 SSR loci and analyzed phylogeographic structuring and the geographic and phylogenetic distribution of GBSSI alleles. We found that GBSSI alleles have distinct spatial distributions and strong associations with particular genetic clusters defined by SSRs. The combination of alleles that results in a partially waxy phenotype does not exist in landrace populations. Our data suggest that broomcorn millet is a system in the process of becoming diploidized for the GBSSI locus responsible for grain amylose. Mutant alleles show some exchange between genetic groups, which was favored by selection for the waxy phenotype in particular regions. Partially waxy phenotypes were probably selected against—this unexpected finding shows that better understanding is needed of the human biology of this phenomenon that distinguishes cereal use in eastern and western cultures.

High-molecular-weight glutenin subunit variation in Turkish emmer wheat [Triticum turgidum L. ssp. dicoccon (Schrank) Thell.] landraces

The genetic diversity of high-molecular-weight (HMW) glutenin subunits in 18 cultivated emmer wheat landrace populations, originating from Turkey, was investigated using sodium dodecyl sulphate polyacrylamide gel electrophoresis. The mean number of alleles (n a) and effective alleles (n ea) were observed as 3.67 and 1.53, respectively. The mean values of expected heterozygosity (gene diversity) (H e) and average heterozygosity (H e,av) were calculated as 0.31 and 0.12, respectively. Actual genetic differentiation (D) and gene flow (N m) between the different populations were observed as 0.24 and 0.16, respectively. Statistical analysis of Pearson’s correlation, multiple regressions and principal component analysis indicated that eco-geographical variables have a significant effect on HMW-glutenin diversity. Considering the dramatic decrease in genetic diversity of modern high-yielding cultivars, the conservation of genetic diversity in these wheat landraces, and in other old cultivars, is important for improving modern monocultures and their ability to resist biotic and abiotic conditions caused by climate changes, thus generating a wide adaption to a variety of environmental conditions. Adoptation measures for germplasm conservation of Turkish emmer wheat landraces and utilisation of their germplasm for improvement of modern wheat varieties were discussed in this study.

Historical genomics of North American maize

Since the advent of modern plant breeding in the 1930s, North American maize has undergone a dramatic adaptation to high-input agriculture. Despite the importance of genetic contributions to historical yield increases, little is known about the underlying genomic changes. Here we use high-density SNP genotyping to characterize a set of North American maize lines spanning the history of modern breeding. We provide a unique analysis of genome-wide developments in genetic diversity, ancestry, and selection. The genomic history of maize is marked by a steady increase in genetic differentiation and linkage disequilibrium, whereas allele frequencies in the total population have remained relatively constant. These changes are associated with increasing genetic separation of breeding pools and decreased diversity in the ancestry of individual lines. We confirm that modern heterotic groups are the product of ongoing divergence from a relatively homogeneous landrace population, but show that differential landrace ancestry remains evident. Using a recent association approach, we characterize signals of directional selection throughout the genome, identifying a number of candidate genes of potential agronomic relevance. However, overall we find that selection has had limited impact on genome-wide patterns of diversity and ancestry, with little evidence for individual lines contributing disproportionately to the accumulation of favorable alleles in today's elite germplasm. Our data suggest breeding progress has mainly involved selection and recombination of relatively common alleles, contributed by a representative but limited set of ancestral lines.

Analysis of average standardized SSR allele size supports domestication of soybean along the Yellow River

Soybean (Glycine max) was domesticated in China from its wild progenitor G. soja. The geographic region of domestication is, however, not exactly known. Here we employed the directional evolution of SSR (microsatellite) repeats (which mutate preferentially into longer alleles) to analyze the domestication process and to infer the most ancestral soybean landraces. In this study, the average standardized SSR allele sizes across 42 SSR loci in 62 accessions of G. soja were determined, and compared with those in 1504 landraces of G. max, collected from all over China and representing the diversity in the gene bank. The standardized SSR allele size in the landraces (0.009) was significantly (P = 8.63 × 10−58) larger than those in G. soja (−0.406). Pairwise comparisons between inferred clusters and sub-clusters of Chinese landraces indicated that the average standardized SSR allele size also increased with the further differentiation of landraces populations. Spring-sowed types had the shortest size, followed by summer-sown types, while the sub-cluster of autumn-sown type had the largest length. The spring-sowed landraces located near the middle region along the Yellow River had the smallest allele sizes, indicating that this is the most ancestral population of cultivated soybean. We concluded that soybean was most likely domesticated in the middle region of the Yellow River in central China, initially as a spring-sown type.

Multivariate Analysis for Quantitative Traits in Finger Millet (Eleusine coracana subsp. coracana) Population Collected from Eastern and Southeastern Africa: Detection for Patterns of Genetic Diversity

genetic variation is a crucial for varietal development and genetic resource conservation. To this regard, a study was conducted at Gute and Arsi Negele (Ethiopia) during 2011 cropping season on one hundred and forty four finger millet landraces collected from different regions of Ethiopia, some introduced from Kenya, Eritrea, Zambia and Zimbabwe to evaluate the genetic diversity for quantitative traits at population level and eco-geographical regions of origin. The trend of quantitative trait diversity revealed that the highest genetic diversity were observed at the lowest level (among landrace populations) followed among the regions or countries of origin and least among altitude classes. This leads to suggest, taking more samples within a locality or population would be a better approach to capture the range of variation in finger millet population. Cluster analysis indicated that finger millet populations from neighboring regions of Ethiopia, neighboring African countries and proximity in altitude classes shared strong similarity. The similarity could be either due to fact that farmer’s selection criteria for a given traits might be similar particularly based on the adaptive role of traits for the environment, the primary seed source can be the same, or high tendency of seed exchange. Principal component analysis at populations level, geographical locations and agro-ecologies of origin indicated that grain yield per plant, thousand grain weight, days to heading, days to maturity, lodging index and biomass weight per plant were the most important traits contributing for the overall variability implying that breeding effort on those traits can meet the targeted objective

Genetic structure and linkage disequilibrium in landrace populations of barley in Sardinia

Multilocus digenic linkage disequilibria (LD) and their population structure were investigated in eleven landrace populations of barley (Hordeum vulgare ssp. vulgare L.) in Sardinia, using 134 dominant simple-sequence amplified polymorphism markers. The analysis of molecular variance for these markers indicated that the populations were partially differentiated (F(ST) = 0.18), and clustered into three geographic areas. Consistent with this population pattern, STRUCTURE analysis allocated individuals from a bulk of all populations into four genetic groups, and these groups also showed geographic patterns. In agreement with other molecular studies in barley, the general level of LD was low (13% of locus pairs, with P < 0.01) in the bulk of 337 lines, and decayed steeply with map distance between markers. The partitioning of multilocus associations into various components indicated that genetic drift and founder effects played a major role in determining the overall genetic makeup of the diversity in these landrace populations, but that epistatic homogenising or diversifying selection was also present. Notably, the variance of the disequilibrium component was relatively high, which implies caution in the pooling of barley lines for association studies. Finally, we compared the analyses of multilocus structure in barley landrace populations with parallel analyses in both composite crosses of barley on the one hand and in natural populations of wild barley on the other. Neither of these serves as suitable mimics of landraces in barley, which require their own study. Overall, the results suggest that these populations can be exploited for LD mapping if population structure is controlled.

Identification of genome-wide variations among three elite restorer lines for hybrid-rice.

Rice restorer lines play an important role in three-line hybrid rice production. Previous research based on molecular tagging has suggested that the restorer lines used widely today have narrow genetic backgrounds. However, patterns of genetic variation at a genome-wide scale in these restorer lines remain largely unknown. The present study performed re-sequencing and genome-wide variation analysis of three important representative restorer lines, namely, IR24, MH63, and SH527, using the Solexa sequencing technology. With the genomic sequence of the Indica cultivar 9311 as the reference, the following genetic features were identified: 267,383 single-nucleotide polymorphisms (SNPs), 52,847 insertion/deletion polymorphisms (InDels), and 3,286 structural variations (SVs) in the genome of IR24; 288,764 SNPs, 59,658 InDels, and 3,226 SVs in MH63; and 259,862 SNPs, 55,500 InDels, and 3,127 SVs in SH527. Variations between samples were also determined by comparative analysis of authentic collections of SNPs, InDels, and SVs, and were functionally annotated. Furthermore, variations in several important genes were also surveyed by alignment analysis in these lines. Our results suggest that genetic variations among these lines, although far lower than those reported in the landrace population, are greater than expected, indicating a complicated genetic basis for the phenotypic diversity of the restorer lines. Identification of genome-wide variation and pattern analysis among the restorer lines will facilitate future genetic studies and the molecular improvement of hybrid rice.

Genetic Diversity and Structure of Pepper (Capsicum AnnuumL.) from Northwestern Mexico Analyzed by Microsatellite Markers

ABSTRACTThe analysis of the variability and genetic structure of wild and landrace populations of pepper (Capsicum annuumL.) is important for the management and conservation of valuable genetic resources and to understand the consequences of domestication on the patterns of neutral genetic variation. For this purpose, 12 populations of wild peppers, 3 landrace populations and 7 hybrid populations from northwestern Mexico were studied using microsatellites. On average, 3.62 alleles per locus were detected in the wild relatives, 3.37 in the landraces, and 3.08 in the hybrids. According to the average values of expected heterozygosity (He), slightly greater genetic diversity was found among the wild relatives (He = 0.466) than in the hybrids (He = 0.440) or the landraces (He = 0.422). In terms of the average number of alleles per locus and the average expected heterozygosity, reductions of 8.18 and 10.25% were found in the genetic diversity of the landraces and hybrids, respectively, with respect to the wild populations. The genetic differentiation among the populations was the highest among hybrids (GST= 0.324), followed by landraces (0.309) and wild relatives (the lowest, at 0.208). Cluster analysis clearly demarcated the wild relatives and domesticated populations into different groups. The high levels of genetic diversity found amongC. annuumin northwestern Mexico suggest that the wild and landrace populations are a valuable resource that should be conserved.

Molecular Characterization, Polymorphism and Association of Porcine IBP4 Gene

The complete coding sequence of the porcine IBP4 gene was isolated using RT-PCR. Sequence analysis showed that the porcine IBP4 gene encodes a protein of 259 amino acids which shares high homology with the insulin-like growth factor binding protein 4 (IBP4) of eight species: cattle (97 %), goat (97 %), chimpanzee (97 %), human (96 %), giant panda (96 %), sheep (95 %), Sumatran orangutan (95 %) and rabbit (93 %). This gene is structured in four exons and three introns as revealed by computer-assisted analysis. Phylogenetic analysis revealed that the porcine IBP4 gene has a close genetic relationship with the IBP4 gene of cattle. Polymorphism analysis indicated that there was an A/G substitution in the position of 134 bp of exon 2 and this mutation did not alter the encoded amino acids of the porcine IBP4 gene. PCR-Hha I-RFLP revealed that eight pig breeds displayed obvious genotype and allele frequency differences at this polymorphic locus. Association of this SNP with litter size traits was assessed in Large White (N = 100) and Landrace (N = 100) populations, and the results demonstrated that this polymorphic locus was significantly associated with the litter size of the first parity in Large White sows and Landrace sows (P &lt;0.05). These data serve as a foundation for further insight into this novel porcine gene.

Diversity and population structure of black soybean landraces originating from Tanba and neighboring regions

Black soybean landraces that had been cultivated in Tanba region and the neighboring regions and conserved black soybean landraces, including those from other regions in Japan, were used in this study. The polymorphisms of 78 SSR markers in nuclear DNA and 6 SSRs in chloroplast DNA were analyzed in the black soybean landrace populations. The result of phylogenic analysis revealed that the black soybeans can be classified into six clades. The landraces originating from Tanba region were classed into first and second clades, and two chloroplast genotypes were found in the population of black soybeans from the Tanba region. Genotype A chloroplast was predominantly identified in major populations of the Tanba, while genotype B was widely distributed in the black soybean population. Population structure analysis in the Japanese black soybean accessions inferred there are six groups. The black soybean landrace from the Tanba region was classified into three groups, mainly corresponding to the distance-based phylogenic results. The two groups were probably derived from different ancestors with Type A and B chloroplast genomes, respectively, whereas the other group showed both types of chloroplast genome. The admixture situations suggested that the landraces in the main group have been widely cultivated in Tanba region, while the landraces that belong to other groups were cultivated in localized area. Several phenotypes were compared among genotype groups, dividing into two sub-groups: founder sub-group and admixed sub-group. Phenotypic differences were observed between founder landraces in group 1 and group 3. On the other hand, landraces in admixture landraces in group 1 and group 2 segregated for several traits, while founder landraces in group 1 were stabled for each trait. These observations suggest that gene flow events have occurred between different founder landraces.

Whole-genome SNP association analysis of reproduction traits in the Finnish Landrace pig breed

BackgroundGood genetic progress for pig reproduction traits has been achieved using a quantitative genetics-based multi-trait BLUP evaluation system. At present, whole-genome single nucleotide polymorphisms (SNP) panels provide a new tool for pig selection. The purpose of this study was to identify SNP associated with reproduction traits in the Finnish Landrace pig breed using the Illumina PorcineSNP60 BeadChip.MethodsAssociation of each SNP with different traits was tested with a weighted linear model, using SNP genotype as a covariate and animal as a random variable. Deregressed estimated breeding values of the progeny tested boars were used as the dependent variable and weights were based on their reliabilities. Statistical significance of the associations was based on Bonferroni-corrected P-values.ResultsDeregressed estimated breeding values were available for 328 genotyped boars. Of the 62 163 SNP in the chip, 57 868 SNP had a call rate > 0.9 and 7 632 SNP were monomorphic. Statistically significant results (P-value < 2.0E-06) were obtained for total number of piglets born in first and later parities and piglet mortality between birth and weaning in later parity, and suggestive associations (P-value < 4.0E-06) for piglet mortality between birth and weaning in first parity, number of stillborn piglets in later parity, first farrowing interval and second farrowing interval. Two of the statistically significant regions for total number of piglets born in first and later parities are located on chromosome 9 around 95 and 79 Mb. The estimated SNP effect in these regions was approximately one piglet between the two homozygote classes. By combining the two most significant SNP in these regions, favourable double homozygote animals are expected to have 1.3 piglets (P-value = 1.69E-08) more than unfavourable double homozygote animals. A region on chromosome 9 (66 Mb) was statistically significant for piglet mortality between birth and weaning in later parity (0.44 piglets between homozygotes, P-value = 6.94E-08).ConclusionsThree separate regions on chromosome 9 gave significant results for litter size and pig mortality. The frequencies of favourable alleles of the significant SNP are moderate in the Finnish Landrace population and these SNP are thus valuable candidates for possible marker-assisted selection.

Population structure of rice (Oryza sativa) landraces from high altitude area of Indian Himalayas

AbstractThis study examined the genetic diversity in 20 rice landrace populations from parts of traditional farming areas of the Indian Himalayas using 11 mapped simple sequence repeats (SSR) loci. Twenty‐four individuals sampled from each of the 20 landraces (480 individuals), which were collected from farmers from Northwest to Northeast Himalaya, showed that all landraces showed within population variation and none were homogeneous. The number of polymorphic loci in a landrace population ranged from 5 to 11. A total of 71 alleles were recorded of which 58 were common and 13 were rare. Of the 71 alleles, 46 were common to both Northwest and Northeast regions, whereas 9 were unique to the former and 16 were unique to the latter. The mean number of alleles per locus was 6.45 and for landrace populations from Northwest and Northeast regions were 5.0 and 5.64, respectively. Population differentiation, as shown by a high FST value (0.61), was greater for Northeast populations. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram classified the populations into three major clusters: cluster I comprised seven populations from the Northwest region, cluster II comprised seven populations from the Northeast region and cluster III comprised populations from both regions. Investigating the population genetic structure can help monitor change in diversity over time and space, and also help devise a rational plan for management of crop landraces on‐farm under farmer management.

Evolutionary history of barley cultivation in Europe revealed by genetic analysis of extant landraces

BackgroundUnderstanding the evolution of cultivated barley is important for two reasons. First, the evolutionary relationships between different landraces might provide information on the spread and subsequent development of barley cultivation, including the adaptation of the crop to new environments and its response to human selection. Second, evolutionary information would enable landraces with similar traits but different genetic backgrounds to be identified, providing alternative strategies for the introduction of these traits into modern germplasm.ResultsThe evolutionary relationships between 651 barley landraces were inferred from the genotypes for 24 microsatellites. The landraces could be divided into nine populations, each with a different geographical distribution. Comparisons with ear row number, caryopsis structure, seasonal growth habit and flowering time revealed a degree of association between population structure and phenotype, and analysis of climate variables indicated that the landraces are adapted, at least to some extent, to their environment. Human selection and/or environmental adaptation may therefore have played a role in the origin and/or maintenance of one or more of the barley landrace populations. There was also evidence that at least some of the population structure derived from geographical partitioning set up during the initial spread of barley cultivation into Europe, or reflected the later introduction of novel varieties. In particular, three closely-related populations were made up almost entirely of plants with the daylength nonresponsive version of the photoperiod response gene PPD-H1, conferring adaptation to the long annual growth season of northern Europe. These three populations probably originated in the eastern Fertile Crescent and entered Europe after the initial spread of agriculture.ConclusionsThe discovery of population structure, combined with knowledge of associated phenotypes and environmental adaptations, enables a rational approach to identification of landraces that might be used as sources of germplasm for breeding programs. The population structure also enables hypotheses concerning the prehistoric spread and development of agriculture to be addressed.