Analysis of line x environment interactions for yield in navy beans. 3. Pattern analysis of environments over years

Yield trials of navy bean (Phaseolus vulgaris L.) lines were grown over a diverse range of locations for 7 years in Queensland, with changes in entries and locations in each year. The yield data were analysed over years using 3 recently developed pattern analysis techniques for the integration of historical, severely unbalanced data from plant breeding programs to derive relationships among environments in the way they discriminate among the entries grown in them. These techniques have been named as cumulative analysis, sequential analysis, and status analysis. The relationships among the locations for testing navy bean lines, although sensitive to the addition of new locations, quickly stabilised. These relationships were related to management (irrigation and row width) and latitude (north v. central v. Kingaroy v. southern Queensland)

Cashmere Marketing is a New Income Source for Central Asian Livestock Farmers

Some indigenous goats in the Central Asian republics of Kazakstan, Kyrgyzstan and Tajikistan produce good quality cashmere (Millar 1986). International processors have recently been buying this cashmere. (Kerven et al., 2005), but Central Asian producers are not equipped to take full advantage of these new marketing opportunities. The U.S. AID Global Livestock-Collaborative Research Support Program project, Developing Institutions and capacity for sheep and fiber marketing in Central Asia is working to increase the income of small-scale livestock farmers through improved cashmere marketing

Approaching public perceptions of datafication through the lens of inequality: a case study in public service media

In the emerging field of critical data studies, there is increasing acknowledgement that the negative effects of datafication are not experienced equally by all. Research on data and discrimination in particular has highlighted how already socially unequal populations are discriminated against in data-driven systems. Elsewhere, there is growing interest in public perceptions of datafication, amongst academic researchers interested in producing ‘bottom up’ understandings of the new roles of data in society and non-academic stakeholders keen to establish positive perceptions of data-driven systems. However, research into public perceptions rarely engages with the issue of inequality which is so central in data and discrimination scholarship. Bringing these two issues together, this paper explores public perceptions of datafication through the lens of inequality, focusing on the relationship between understandings and feelings within these perceptions. The paper draws on empirical focus group research into how audiences perceive the data practices that signing in to access BBC digital services enable. The paper shows how inequalities relating to age, dis/ability, poverty and their intersections played a role in shaping perceptions and that these social inequalities informed understandings of and feelings about data practices in complex and diverse ways. It concludes with reflections on the significance of these findings for future research and for data-related policy

Biodiversity Management in Chickpea

This chapter focuses on the management of biodiversity in chickpea. The morphological diversity; germplasm collections and enhancement; core and minicore collections and their use for diversity studies and new breeding goals; and the conservation and documentation of chickpea genetic resources are describe

Legume Crops Phylogeny and Genetic Diversity for Science and Breeding

Economically, legumes (Fabaceae) represent the second most important family of crop plants after the grass family, Poaceae. Grain legumes account for 27% of world crop production and provide 33% of the dietary protein consumed by humans, while pasture and forage legumes provide vital part of animal feed. Fabaceae, the third largest family of flowering plants, has traditionally been divided into the following three subfamilies: Caesalpinioideae, Mimosoideae, and Papilionoideae, all together with 800 genera and 20,000 species. The latter subfamily contains most of the major cultivated food and feed crops. Among the grain legumes are some of mankind's earliest crop plants, whose domestication parallelled that of cereals: Soybean in China; faba bean, lentil, chickpea and pea in the Fertile Crescent of the Near East; cowpeas and bambara groundnut in Africa; soybean and mungbeans in East Asia; pigeonpea and the grams in South Asia; and common bean, lima bean, scarlet runner bean, tepary bean and lupin in Central and South America. The importance of legumes is evidenced by their high representation in ex situ germplasm collections, with more than 1,000,000 accessions worldwide. A detailed knowledge of the phylogenetic relationships of the Fabaceae is essential for understanding the origin and diversification of this economically and ecologically important family of angiosperms. This review aims to combine the phylogenetic and genetic diversity approaches to better illustrate the origin, domestication history and preserved germplasm of major legume crops from 13 genera of six tribes and to indicate further potential both for science and agriculture.</p

A unified framework for multi-locus association analysis of both common and rare variants

<p>Abstract</p> <p>Background</p> <p>Common, complex diseases are hypothesized to result from a combination of common and rare genetic variants. We developed a unified framework for the joint association testing of both types of variants. Within the framework, we developed a union-intersection test suitable for genome-wide analysis of single nucleotide polymorphisms (SNPs), candidate gene data, as well as medical sequencing data. The union-intersection test is a composite test of association of genotype frequencies and differential correlation among markers.</p> <p>Results</p> <p>We demonstrated by computer simulation that the false positive error rate was controlled at the expected level. We also demonstrated scenarios in which the multi-locus test was more powerful than traditional single marker analysis. To illustrate use of the union-intersection test with real data, we analyzed a publically available data set of 319,813 autosomal SNPs genotyped for 938 cases of Parkinson disease and 863 neurologically normal controls for which no genome-wide significant results were found by traditional single marker analysis. We also analyzed an independent follow-up sample of 183 cases and 248 controls for replication.</p> <p>Conclusions</p> <p>We identified a single risk haplotype with a directionally consistent effect in both samples in the gene <it>GAK</it>, which is involved in clathrin-mediated membrane trafficking. We also found suggestive evidence that directionally inconsistent marginal effects from single marker analysis appeared to result from risk being driven by different haplotypes in the two samples for the genes <it>SYN3 </it>and <it>NGLY1</it>, which are involved in neurotransmitter release and proteasomal degradation, respectively. These results illustrate the utility of our unified framework for genome-wide association analysis of common, complex diseases.</p

Systemic properties of metabolic networks lead to an epistasis-based model for heterosis

The genetic and molecular approaches to heterosis usually do not rely on any model of the genotype–phenotype relationship. From the generalization of Kacser and Burns’ biochemical model for dominance and epistasis to networks with several variable enzymes, we hypothesized that metabolic heterosis could be observed because the response of the flux towards enzyme activities and/or concentrations follows a multi-dimensional hyperbolic-like relationship. To corroborate this, we used the values of systemic parameters accounting for the kinetic behaviour of four enzymes of the upstream part of glycolysis, and simulated genetic variability by varying in silico enzyme concentrations. Then we “crossed” virtual parents to get 1,000 hybrids, and showed that best-parent heterosis was frequently observed. The decomposition of the flux value into genetic effects, with the help of a novel multilocus epistasis index, revealed that antagonistic additive-by-additive epistasis effects play the major role in this framework of the genotype–phenotype relationship. This result is consistent with various observations in quantitative and evolutionary genetics, and provides a model unifying the genetic effects underlying heterosis

The Nuclear Transcription Factor PKNOX2 Is a Candidate Gene for Substance Dependence in European-Origin Women

Substance dependence or addiction is a complex environmental and genetic disorder that results in serious health and socio-economic consequences. Multiple substance dependence categories together, rather than any one individual addiction outcome, may explain the genetic variability of such disorder. In our study, we defined a composite substance dependence phenotype derived from six individual diagnoses: addiction to nicotine, alcohol, marijuana, cocaine, opiates or other drugs as a whole. Using data from several genomewide case-control studies, we identified a strong (Odds ratio  = 1.77) and significant (p-value = 7E-8) association signal with a novel gene, PBX/knotted 1 homeobox 2 (PKNOX2), on chromosome 11 with the composite phenotype in European-origin women. The association signal is not as significant when individual outcomes for addiction are considered, or in males or African-origin population. Our findings underscore the importance of considering multiple addiction types and the importance of considering population and gender stratification when analyzing data with heterogeneous population