Posts Tagged ‘Genetic’

Genetic diversity of tropical early-maturing maize inbreds and theirperformance in hybrid combinations under drought and optimum growing conditions

Posted by gabrielamartinez on , in Journal Articles

56902Authors: Oyekunle, M., Badu-Apraku, B., Franco, J., Hearne, S.

Published in: Field Crops Research 2014, vol. 170, p. 55-65.


Hybrid development is enhanced by the assessment and understanding of genetic diversity and dis-tance within inbreds. One hundred and fifty hybrids derived from 30 early-maturing inbreds plus sixchecks were evaluated at three locations in Nigeria for 2 years to assess their performance under droughtand well-watered conditions. In addition, twenty three microsatellite markers were employed to assessgenetic diversity of selected 42 inbreds. Significant differences were observed among inbreds and hybridsfor most traits under both research conditions. A total of 130 alleles were detected ranging from two fornc133 to nine for phi299852 with an average of 5.7 alleles per locus. Polymorphic information contentranged from 0.17 for phi308707 to 0.77 for phi084 with an average of 0.54. Thirty-one unique alleleswere detected in 21 inbreds. Microsatellite markers classified the inbred lines into five groups. Geneticdistance estimates among pairs of inbreds ranged from 0.42 (TZEI 26 vs TZEI 108) to 0.85 (TZEI 24 vs TZEI4) with an average of 0.67. Correlation between microsatellite-based GD estimates of the parental linesand their F1hybrids were not significant for grain yield and other traits under drought and well-wateredconditions. However, significant correlations existed between F1hybrid grain yield and heterosis underdrought and well-watered conditions. TZEI 31 × TZEI 18 was identified as the highest-yielding and stablehybrid across environments and should be promoted for adoption by farmers in West and Central Africa.

Studies of the genetics of inheritance of stem rust resistance in bread wheat

Posted by Carelia Juarez on , in Journal Articles

Published in African Journal of Biotechnology 12 (21) : 3153-3159, 2013

Nzuve, F. M.; Tusiime, G.; Bhavani, S.; Njau, P. N.; Wanyera, R.

Pgt race TTKSK (Ug99) has a wide virulence range with respect to currently grown wheat cultivars worldwide. Aspects of migration, mutation, recombination and selection in the pathogen have led to previously deployed stem rust resistance genes being ineffective. Race TTKSK has further evolved to acquire virulence for resistance genes such as Sr24 (race Ug99 + Sr24) and Sr36 (Ug99 + Sr36). Five resistant wheat lines (KSL-2, KSL-3, KSL-5, KSL-12 and KSL-19) which were resistant in tests during 2008, 2009 and 2010 were used as parents in crosses with stem rust susceptible line CACUKE to develop genetic populations for determining the inheritance of resistance to stem rust. F3 populations were evaluated at KARI Njoro in the 2012 off season and 2012 to 2013 main season. The adult plant stem rust responses were scored using the modified Cobb’s scale. The F2:3 lines of population(s) exhibiting qualitative variation were grouped as homozygous resistant (HR), segregating (Seg) and homozygous susceptible (HS). Heavy disease pressure was present during the cropping seasons with the check CACUKE displaying 90% susceptibility. Chi square analysis revealed that the segregation data in the parent KSL-2 did not deviate significantly from the single gene model (1:2:1) suggesting that the resistance to stem rust is conditioned by a single dominant gene. The Chi square test also revealed that the stem rust resistance in the parents KSL-3, KSL-5, KSL-12 and KSL-19 was conditioned by two genes. The families from the KSL-2 and KSL-3 crosses also segregated for the presence of the pseudo black chaff implying that theSr2 gene could be present in the background of these wheat parents. The superior transgressive segregants identified in these crosses will be used in breeding.

Genetic protection of wheat from rusts and development of resistant varieties in Russia and Ukraine

Posted by on , in Journal Articles

Published in Euphytica 179(2): 297-311, 2011

Genetic protection of wheat from rusts and development of resistant varieties in Russia and Ukraine

A. Morgounov, I. Ablova, O. Babayants, L. Babayants, L. Bespalova, Zh. Khudokormov, N. Litvinenko, V. Shamanin and V. Syukov

Leaf rust represents the major threat to wheat production in Russia and Ukraine. It has been present for many years and epidemics of the pathogen occur in different regions on both winter and spring wheat. In some regions there is evidence of more frequent epidemics, probably due to higher precipitation as a result of climate change. There is evidence that the virulence of the leaf rust population in Ukraine and European Russia and on winter wheat and spring wheat is similar. The pathogen population structure in Western Siberia is also similar to the European part, although there are some significant differences based on the genes employed in different regions. Ukrainian wheat breeders mostly rely on major resistance genes from wide crosses and have succeeded in developing resistant varieties. The North Caucasus winter wheat breeding programs apply the strategy of deploying varieties with different types of resistance and genes. This approach resulted in decreased leaf rust incidence in the region. Genes Lr23 and Lr19 deployed in spring wheat in the Volga region were rapidly overcome by the pathogen. There are continuing efforts to incorporate resistance from wild species. The first spring wheat leaf rust resistant varieties released in Western Siberia possessed gene LrTR which protected the crop for 10–15 years, but was eventually broken in 2007. Slow rusting is being utilized in several breeding programs in Russia and Ukraine, but has not become a major strategy.

Genetic distance and hybrid value in tropical maize under P stress and non stress conditions in acid soils

Posted by on , in Journal Articles

Published in Euphytica 178(1): 99-109, 2011

Genetic distance and hybrid value in tropical maize under P stress and non stress conditions in acid soils

M. L. C. George, F. Salazar, M. Warburton, L. Narro and F. A. Vallejo

An emphasis in maize breeding for areas with acid soils is the development of varieties with tolerance to P-deficiency plus high yield potential in acidic as well as normal soils. This study was carried out to assess the (i) genetic diversity within a set of tropical inbred lines developed from acid soil-tolerant populations; (ii) F1 yield performance, mid-parent heterosis (MPH), high-parent heterosis (HPH), and specific combining ability (SCA) in a diallel set of crosses under P stress (low P) and non-stress (high P) conditions; and (iii) the effect of P stress on the relationship between genetic distance (GD) and hybrid performance. Using field evaluation and molecular marker studies, the results show that these germplasm from the South American maize breeding program of CIMMYT for improving tolerance to acid soils had only a moderate level of genetic diversity. The utility of GD as a predictor of hybrid value is best up to a certain threshold, as correlations with GD became inconsistent when the inbred parents were greatly divergent. There was no correlation between GD and F1 grain yield, MPH, HPH and SCA when the GD was >0.77. The high correlation of GD with F1 grain yield and with SCA in specific subsets of crosses having a narrower range of GD shows that GD can be put to practical use in predicting hybrid performance. The highest correlation between GD and SCA, seen in the subset of crosses between lines within a cluster, was reasonably stable even when the environment had a severe effect on yield.

Association mapping for enhancing maize (Zea mays L.) genetic improvement

Posted by on , in Journal Articles

Published in Crop Science 51(2); 17 p, 2011

Association mapping for enhancing maize (Zea mays L.) genetic improvement

Yan, J.; Warburton, M.; Crouch, J.

Association mapping through linkage disequilibrium (LD) analysis is a powerful tool for the dissection of complex agronomic traits and for the identification of alleles that can contribute to the enhancement of a target trait. With the developments of high throughput genotyping techniques and advanced statistical approaches as well as the assembling and characterization of multiple association mapping panels, maize has become the model crop for association analysis. In this paper, we summarize progress in maize association mapping and the impacts of genetic diversity, rate of LD decay, population size, and population structure. We also review the use of candidate genes and gene-based markers in maize association mapping studies that has generated particularly promising results. In addition, we examine recent developments in genome-wide genotyping techniques that promise to improve the power of association mapping and significantly refine our understanding of the genetic architecture of complex quantitative traits. The new challenges and opportunities associated with genome-wide analysis studies are discussed. In conclusion, we review the current and future impacts of association mapping on maize improvement along with the potential benefits for poor people in developing countries who are dependent on this crop for their food security and livelihoods.

Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought

Posted by on , in Journal Articles

Published in Journal of Experimental Botany 62(2):701-716, 2011

Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought

Setter, T.L.; Jianbing Yan; Warburton, M.; Ribaut, J-M; Yunbi Xu; Sawkins, M.; Buckler, E.S.; Zhiwu Zhang; Gore, M.A.

In maize, water stress at flowering causes loss of kernel set and productivity. While changes in the levels of sugars and abscisic acid (ABA) are thought to play a role in this stress response, the mechanistic basis and genes involved are not known. A candidate gene approach was used with association mapping to identify loci involved in accumulation of carbohydrates and ABA metabolites during stress. A panel of single nucleotide polymorphisms (SNPs) in genes from these metabolic pathways and in genes for reproductive development and stress response was used to genotype 350 tropical and subtropical maize inbred lines that were well watered or water stressed at flowering. Pre-pollination ears, silks, and leaves were analysed for sugars, starch, proline, ABA, ABA-glucose ester, and phaseic acid. ABA and sugar levels in silks and ears were negatively correlated with their growth. Association mapping with 1229 SNPs in 540 candidate genes identified an SNP in the maize homologue of the Arabidopsis MADS-box gene, PISTILLATA, which was significantly associated with phaseic acid in ears of well-watered plants, and an SNP in pyruvate dehydrogenase kinase, a key regulator of carbon flux into respiration, that was associated with silk sugar concentration. An SNP in an aldehyde oxidase gene was significantly associated with ABA levels in silks of water-stressed plants. Given the short range over which decay of linkage disequilibrium occurs in maize, the results indicate that allelic variation in these genes affects ABA and carbohydrate metabolism in floral tissues during drought.

New Book in the Library: Genetic data analysis II: methods for discrete population genetic data

Posted by Jose Juan Caballero on , in New Acquisitions

Genetic Data Analysis II:  methods for discrete population genetic data

 Bruce S. Weir

ISBN-13: 978-0878939022

Genetic Data Analysis, first published in 1990, became the standard reference for ways to interpret discrete population genetic data. Genetic Data Analysis II retains the strengths of the original book and, based upon the suggestions of users, includes many new features, notably the revision of Chapter 10 (Phylogeny Reconstruction) to incorporate newer methods, and new chapters on Linkage and Individual Identification.

Genetic Data Analysis II features an expanded set of Exercises, with solutions, and an expanded list of references. In addition, a suite of Windows-based programs written by Paul O. Lewis and Dmitri Zaykin is available without charge from the Web site maintained by the program in Statistical Genetics at North Carolina State University.

Hierarchical Multiple-Factor Analysis for Classifying Genotypes Based on Phenotypic and Genetic Data

Posted by on , in Journal Articles

Published in Crop Science 50(1):105-117, 2010

Hierarchical Multiple-Factor Analysis for Classifying Genotypes Based on Phenotypic and Genetic Data

Jorge Franco, José Crossa and Santosh Desphande

A numerical classification problem encountered by breeders and gene-bank curators is how to partition the original heterogeneous population of genotypes into non-overlapping homogeneous subpopulations. The measure of distance that may be defined depends on the type of variables measured (i.e., continuous and/or discrete). The key points are whether and how a distance may be defined using all types of variables to achieve effective classification. The objective of this research was to propose an approach that combines the use of hierarchical multiple-factor analysis (HMFA) and the two-stage Ward Modified Location Model (Ward-MLM) classification strategy that allows (i) combining different types of phenotypic and genetic data simultaneously; (ii) balancing out the effects of the different phenotypic, genetic, continuous, and discrete variables; and (iii) measuring the contribution of each original variable to the new principal axes (PAs). Of the two strategies applied for developing PA scores to be used for clustering genotypes, the strategy that used the first few PA scores to which phenotypic and genetic variables each contributed 50% (i.e., a balanced contribution) formed better groups than those formed by the strategy that used a large number of PA scores explaining 95% of total variability. Phenotypic variables account for much variability in the initial PA; then their contributions decrease. The importance of genetic variables increases in later PAs. Results showed that various phenotypic and genetic variables made important contributions to the new PA. The HMFA uses all phenotypic and genetic variables simultaneously and, in conjunction with the Ward-MLM method, it offers an effective unifying approach for the classification of breeding genotypes into homogeneous groups and for the formation of core subsets for genetic resource conservation.

Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures

Posted by on , in Journal Articles

Published in BMC Bioinformatics 10:243, 2009

Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures

Chris Thachuk , José Crossa , Jorge Franco, Susanne Dreisigacker, Marilyn Warburton,  Guy F Davenport


Existing algorithms and methods for forming diverse core subsets currently address either allele representativeness (breeder’s preference) or allele richness (taxonomist’s preference). The main objective of this paper is to propose a powerful yet flexible algorithm capable of selecting core subsets that have high average genetic distance between accessions, or rich genetic diversity overall, or a combination of both.


We present Core Hunter, an advanced stochastic local search algorithm for selecting core subsets. Core Hunter is able to find core subsets having more genetic diversity and better average genetic distance than the current state-of-the-art algorithms for all genetic distance and diversity measures we evaluated. Furthermore, Core Hunter can attempt to optimize any number of genetic measures simultaneously, based on the preference of the user. Notably, Core Hunter is able to select significantly smaller core subsets, which retain all unique alleles from a reference collection, than state-of-the-art algorithms.


Core Hunter is a highly effective and flexible tool for sampling genetic resources and establishing core subsets. Our implementation, documentation, and source code for Core Hunter is available at

New article from CIMMYT – Estimating maize genetic erosion in modernized smallholder agriculture

Posted by on , in Journal Articles

Published in Theoretical and Applied Genetics 119(5): 875-888 (2009)

Estimating maize genetic erosion in modernized smallholder agriculture

Joost van Heerwaarden, J. Hellin, R. F. Visser and F. A. van Eeuwijk

Abstract: Replacement of crop landraces by modern varieties is thought to cause diversity loss. We studied genetic erosion in maize within a model system; modernized smallholder agriculture in southern Mexico. The local seed supply was described through interviews and in situ seed collection. In spite of the dominance of commercial seed, the informal seed system was found to persist. True landraces were rare and most informal seed was derived from modern varieties (creolized). Seed lots were characterized for agronomical traits and molecular markers. We avoided the problem of non-consistent nomenclature by taking individual seed lots as the basis for diversity inference. We defined diversity as the weighted average distance between seed lots. Diversity was calculated for subsets of the seed supply to assess the impact of replacing traditional landraces with any of these subsets. Results were different for molecular markers, ear- and vegetative/flowering traits. Nonetheless, creolized varieties showed low diversity for all traits. These varieties were distinct from traditional landraces and little differentiated from their ancestral stocks. Although adoption of creolized maize into the informal seed system has lowered diversity as compared to traditional landraces, genetic erosion was moderated by the distinct features offered by modern varieties.