Posts Tagged ‘Genetic diversity’

Genetic diversity analysis reveals importance of Green Revolution Gene (Sd1 Locus) for drought tolerance in rice

Posted by gabrielamartinez on , in Journal Articles

57499Authors: Vikram, P.; Kadam, S; Singh, B.P; You Jin lee; Jitendra Kumar Pal; Singh, S; Singh, O.N; Mallikarjuna Swamy, B.P; Thiyagarajan, K; Sukhwinder-Singh; Singh, N.K.

Published in: Agricultural Research, In press.


Genetic diversity analysis based on genome-wide single-nucleotide polymorphism (SNP) assay of a set of Indian rice cultivars including modern high-yielding varieties and landraces revealed two broad groups, one with “Aus” and the other with “Indica” cultivars. Marker analysis of these genotypes was carried out for three major drought tolerance QTLs as well as green revolution gene, sd1. This gene collocates with a drought QTL, qDTY 1.1 . The well-known drought-tolerant landraces or traditional varieties had the “tall” allele of the sd1 gene, indicating the possibility of close linkage, pleiotropy or both associated with this gene. Profiling of rice genotypes investigated in the present study with drought QTL markers, genome-wide SNPs, and sd1 gene reveals the importance of using multiple genes rather focusing on any single major QTL/gene for drought tolerance. Our results suggested that rice genetic improvement for rain-fed areas require enhanced use of pre-green revolution varieties.

Genetic relationships and structure among open-pollinated maize varieties adapted to eastern and southern Africa using microsatellite markers

Posted by Carelia Juarez on , in Journal Articles

Published in Molecular Breeding, 2014

Fentaye Kassa SemagnMagorokosho, C.Ogugo, V.Makumbi, D.Warburton, M.L.

Molecular characterization of open-pollinated maize varieties (OPVs) is fundamentally important in maize germplasm improvement. We investigated the extent of genetic differences, patterns of relationships, and population structure among 218 diverse OPVs widely used in southern and eastern Africa using the model-based population structure, analysis of molecular variance, cluster analysis, principal component analysis, and discriminant analysis. The OPVs were genotyped with 51 microsatellite markers and the fluorescent detection system of the Applied Biosystems 3730 Capillary Sequencer. The number of alleles detected in each OPV varied from 72 to 155, with an overall mean of 127.6. Genetic distance among the OPVs varied from 0.051 to 0.434, with a mean of 0.227. The different multivariate methods suggest the presence of 2–4 possible groups, primarily by maturity groups but also with overlapping variation between breeding programs, mega-environments, and specific agronomic traits. Nearly all OPVs in group 1 and group 2 belong to the intermediate-late and early maturity groups, respectively. Group 3 consisted of mainly intermediate maturing OPVs, while group 4 contained OPVs of different maturity groups. The OPVs widely used in eastern Africa either originated from the southern African maize breeding programs, or the majority of inbred lines used as parents by the two breeding programs in developing the OPVs might be genetically related. Some of the OPVs are much older than others, but they still did not show a clear pattern of genetic differentiation as compared with the recently developed ones, which is most likely due to recycling of the best parental lines in forming new OPVs.

Diversidad genetica en maices nativos mexicanos tropicales. Genetic diversity in tropical Mexican landraces of maize

Posted by Carelia Juarez on , in Journal Articles

Published in Revista Fitotecnia Mexicana 36 (Supl. 3-A) : 329-338, 2013

Gonzalez Castro, M.E.; Palacios Rojas, N.; Espinoza Banda, A.; Bedoya Salaza, C.A.

Mexico is considered the center of origin and domestication of maize (Zea mays L.), and it is recognized as one of the most important centers of diversity. Evaluation of native maize diversity is specially important for conservation strategies design, germplasm characterization and its use in breeding; native maize is potentially a source of new, favorable and exotic features. In this study, 30 microsatellite molecular markers were tested to characterize intraracial and between population genetic diversity present in 196 tropical populations representing 20 corn races. Results indicated that these accessions can be grouped into three ecological areas: Gulf of México, South Pacific and Yucatán Peninsula (A), the Northwestern and Western (B), and Intermediate Lowland Oaxaca and Chiapas (C). Average number of alleles per locus within the populations was 9. Average genetic diversity of 20 tropical Mexican maize races was 0.57 across all accessions. There was greater variability among races (23.18) than within each race (0.99 to 8.72). Genetic erosion due to limited geographical distribution for Zapalote and Jala races was evident, thus indicating the need for preservation efforts. Genetic diversity indices of 0.53 found for Tuxpeño germplasm confirm that although they have been widely used in breeding programs, there is untapped diversity in this race.

High genetic diversity of Mycospaherella graminicola (Zymoseptoria tritici) from a single wheat field in Tunisia as revealed by SSR markers

Posted by Carelia Juarez on , in Journal Articles

Published in Journal of Biotechnology 12 (12) : 1344-1349, 2013

Samia Berraies, Mohamed Salah Gharbi, François Belzile, Amor Yahyaoui, Mohamed Rebah Hajlaoui, Mokhtar Trifi, Martine Jean and Salah Rezgui

Microsatellite markers were used to assess genetic diversity of Mycosphaerella graminicola at a micro geographical scale in Tunisia. Forty five (45) isolates were sampled and assessed using seven pairs of single-locus microsatellite primers not previously tested on populations of M. graminicola in Tunisia. Genetic diversity of the field population ranged from 0.403 to 0.555 with an average of 0.484. A high level of genetic diversity was found at a sharp scale throughout the pathogen population tested. Among 45 isolates sampled, 39 different multi locus genotypes (MLG) were identified. Cluster analysis (UPGMA) showed that 86% of the isolates tested were distinct. The high degree  of DNA polymorphism, the large number of different molecular genotypes and the pattern of cluster analysis suggest that sexual ascospores and/or asexual spores of a highly mutable local population could have contributed to the genetic diversity of M. graminicola in Tunisia.

Genetic interrelationships among medium to late maturing tropical maize inbred lines using selected SSR markers

Posted by Carelia Juarez on , in Journal Articles

Published in Euphytica 191 (2) : 269-277, 2013

Abera Wende, Hussein Shimelis, John Derera, Worku Mosisa, Jedidah Danson and Mark D. Laing

Understanding the genetic relationships among breeding lines is fundamental in crop improvement programs. The objectives of this study were to apply selected polymorphic single sequence repeat (SSR) DNA markers and cluster medium to late maturing tropical elite maize inbred lines for effective hybrid breeding. Twenty elite inbred lines were genotyped with 20 SSR markers. The analysis detected a total of 108 alleles. The unweighted pair group method with arithmetic mean allocated the inbred lines into five clusters consistent with the known pedigrees. The tested inbred lines that were adapted to mid-altitude, sub-humid agro-ecologies were classified in different clusters, except for a few discrepancies. The greatest genetic distance was identified between the clusters of lines CML-202 and Gibe-1-91-1-1-1-1. The analysis determined the genetic grouping present in the source population, which will assist in effective utilization of the lines in tropical hybrid maize breeding  programs to exploit heterosis.

Genetic diversity of Pyrenophora tritici-repentis in Algeria as revealed by amplified fragement length polymorphism (AFLP) analysis

Posted by Carelia Juarez on , in Journal Articles

Published in Journal of Biotechnology 12 (26) : 4082-4093, 2013

Hamida Benslimane, Samer Lababidi, Amor Yahyaoui, Francis Ogbonnaya, Zouaoui Bouznad and Micheal Baum

Tan spot caused by Pyrenophora tritici-repentis is a major wheat disease. DNA of 61 isolates of P. tritici-repentis from different cereal growing areas in Algeria were analyzed using amplified fragment length polymorphism (AFLP) in order to  study the genetic diversity among this population. Initially, 78 primer combinations were tested, of which 12 were selected and applied to the 61 isolates. There was a high genetic diversity in this population of P. tritici-repentis with 61 different haplotypes among the 61 isolates selected. The Jaccard similarity index range was 1.43 to 68.37%. Cluster analysis showed that, clustering of isolates was independent of their race classification, geographic origin, or host plant. However, one isolate (Ptr24) that showed a new virulence pattern in our previous race analysis study was clearly distinguished from the rest of the population studied. This isolate had not only new virulence but also different genetic makeup to other P. tritici-repentis isolates and requires additional studies to decipher complete knowledge of host-pathogen interactions for tan spot of wheat.

Cell wall composition and biomass digestibility diversity in Mexican maize (Zea mays L) landraces and CIMMYT inbred lines

Posted by Carelia Juarez on , in Journal Articles

Published in Maydica 58 (1) : 21-33, 2013

German Muttoni, Natalia Palacios-Rojas, Luis Galicia, Aldo Rosales, Kevin V. Pixley and Natalia de Leon

Maize is one of the most important crops worldwide. Historically, breeding efforts in this crop have been primarily focused on the improvement of grain yield and stability and just recently also on the potential utility of maize stover (above ground biomass excluding the grain) as a source of biomass for the production of feed, fiber and cellulosic ethanol. The International Maize and Wheat Improvement Center (CIMMYT) holds one of the largest maize germplasm collections in the world and therefore is an important source of phenotypic and genetic diversity for many traits. Our objectives were to assess the phenotypic diversity for cell wall composition and biomass digestibility in Mexican tropical, subtropical and highland maize landraces and elite maize lines (CMLs) in the CIMMYT germplasm collection, as well as to evaluate the relationship between place of origin of these materials and phenotypic expression of biomass compositional traits. The range of variation for neutral detergent fiber for three groups of landraces was from 47 to 73%. Slightly larger levels of phenotypic variation were observed for this trait in the set of CMLs evaluated (42 to 78%). Some of the inbred lines, such as CML 507, presented superior characteristics in terms of cell wall composition and digestibility. The Tuxpeño tropical-subtropical race, widely used in CIMMYT breeding programs, formed a cluster characterized by high cell wall content and low biomass digestibility. The CIMMYT germplasm collection appears to be a vast source of untapped genetic and phenotypic variation for the improvement of maize biomass composition.

Molecular genetic diversity analysis in emmer wheat (Triticum dicoccon Schrank) from India

Posted by Carelia Juarez on , in Journal Articles

Published in Genetic Resources and Crop Evolution 60 (1) : 165-174, 2013

Arvindkumar Salunkhe, Shubhada Tamhankar, Sujata Tetali, Maria Zaharieva, David Bonnett, Richard Trethowan and Satish Misra

Emmer wheat (Triticum dicoccon Schrank) is still largely cultivated in India, and highly appreciated for the preparation of traditional dishes. Moreover, its nutritional characteristics could justify a development of its cultivation. The perspective of genetic improvement however requires a good knowledge of the genetic diversity existing within the eco-geographic group of Indian emmer wheats. A set of 48 emmer wheat accessions from India including 28 from a local collection and 20 Indian accessions obtained from CIMMYT, Mexico, was assessed for genetic variability using 47 microsatellite (SSR) markers, distributed over all the 14 chromosomes. The number of alleles per locus ranged from 2 to 9, with an average of 3.87 alleles per locus. A total of 201 alleles were detected at 52 loci with average polymorphic information content of 0.35 per locus and a mean resolving power of 1. The pair-wise similarity coefficients calculated from binary data matrix based on presence or absence of alleles varied from 0.15 to 0.98, but was greater than 0.5 for most accessions, indicating a high level of similarity. A cluster analysis based on the similarity matrix identified nine distinct accessions and three clusters. All the recently developed commercial varieties were distinctly different from the clusters. Based on the analysis, it appears that Indian emmer wheats are not very diverse. Consequently, there is a need to increase the diversity within the Indian emmer wheat eco-geographic group, by introducing diversity from other eco-geographic groups, or even from other wheat species.

Microsatellite marker-based diversity and population genetic analysis of selected lowland and mid-altitude maize landrace accessions of India

Posted by Carelia Juarez on , in Journal Articles

Published in Journal of Plant Biochemistry and Biotechnology, 2012

Samanthi K. Wasala and B. M. Prasanna

Maize (Zea mays L.) harbours significant genetic diversity not only in its centre of origin (Mexico) but also in several countries worldwide, including India, in the form of landraces. In this study, DNA fingerprinting of 48 landrace accessions from diverse regions of India was undertaken using 42 fluorescent dye-labeled Simple Sequence Repeat (SSR) markers, followed by allele resolution using DNA sequencer and analysis of molecular diversity within and among these landraces. The study revealed a large number of alleles (550), with high mean number of alleles per locus (13.1), and Polymorphism Information Content (PIC) of 0.60, reflecting the level of diversity in the landrace accessions. Besides identification of 174 unique alleles in 44 accessions, six highly frequent SSR alleles were detected at six loci (phi014, phi090, phi112, umc1367, phi062 and umc1266) with individual frequencies greater than 0.75, indicating that chromosomal regions harboring these SSR alleles are not selectively neutral. F statistics revealed very high genetic differentiation, population subdivision and varying levels of inbreeding in the landraces. Analysis of Molecular Variance showed that 63 % of the total variation in the accessions could be attributed to within-population diversity, and 37 % represented between population diversity. Cluster analysis of SSR data using Nei’s genetic distance and UPGMA revealed considerable genetic diversity in these populations, although no clear separation of accessions was observed based on their geographic origin.


Comparative SNP and Haplotype Analysis Reveals a Higher Genetic Diversity and Rapider LD Decay in Tropical than Temperate Germplasm in Maize

Posted by on , in Journal Articles

Published in PLoS One 6(9); 8p. 2011 

Comparative SNP and Haplotype Analysis Reveals a Higher Genetic Diversity and Rapider LD Decay in Tropical than Temperate Germplasm in Maize.

Yanli Lu, Trushar Shah, Zhuanfang Hao, Suketoshi Taba, Shihuang Zhang, Shibin Gao, Jian Liu, Moju Cao, Jing Wang, A. Bhanu Prakash Tingzhao Rong, Yunbi Xu

Understanding of genetic diversity and linkage disequilibrium (LD) decay in diverse maize germplasm is fundamentally important for maize improvement. A total of 287 tropical and 160 temperate inbred lines were genotyped with 1943 single nucleotide polymorphism (SNP) markers of high quality and compared for genetic diversity and LD decay using the SNPs and their haplotypes developed from genic and intergenic regions. Intronic SNPs revealed a substantial higher variation than exonic SNPs. The big window size haplotypes (3-SNP slide-window covering 2160 kb on average) revealed much higher genetic diversity than the 10 kb-window and gene-window haplotypes. The polymorphic information content values revealed by the haplotypes (0.436–0.566) were generally much higher than individual SNPs (0.247–0.259). Cluster analysis classified the 447 maize lines into two major groups, corresponding to temperate and tropical types. The level of genetic diversity and subpopulation structure were associated with the germplasm origin and post-domestication selection. Compared to temperate lines, the tropical lines had a much higher level of genetic diversity with no significant subpopulation structure identified. Significant variation in LD decay distance (2–100 kb) was found across the genome, chromosomal regions and germplasm groups. The average of LD decay distance (10–100 kb) in the temperate germplasm was two to ten times larger than that in the tropical germplasm (5–10 kb). In conclusion, tropical maize not only host high genetic diversity that can be exploited for future plant breeding, but also show rapid LD decay that provides more opportunity for selection.