Statistical Theory and Methods for Evolutionary Genomics

Xun Gu
ISBN: 9780199213269
Oxford University Press
DOI: 10.1093/acprof:oso/9780199213269.003.0010

Evolutionary genomics is a relatively new research field with the ultimate goal of understanding the underlying evolutionary and genetic mechanisms for the emergence of genome complexity under changing environments. It stems from an integration of high throughput data from functional genomics, statistical modelling and bioinformatics, and the procedure of phylogeny-based analysis. This book summarises the statistical framework of evolutionary genomics, and illustrates how statistical modelling and testing can enhance our understanding of functional genomic evolution. The book reviews the recent developments in methodology from an evolutionary perspective of genome function, and incorporates substantial examples from high throughput data in model organisms. In addition to phylogeny-based functional analysis of DNA sequences, the book includes discussion on how new types of functional genomic data (e.g., microarray) can provide exciting new insights into the evolution of genome function, which can lead in turn to an understanding of the emergence of genome complexity during evolution.

Calvin Dytham
ISBN: 978-1-4051-9839-4
John Wiley & Sons
320 pages

Published in Journal of Pest Science 85 (2): 267-275, 2012

J. K. Mwololo, S. N. Mugo, T. Tefera, P. Okori, S. W. Munyiri, K. Semagn, M. Otim and Y. Beyene

Post-harvest losses caused by the larger grain borer (LGB, Prostephanus truncatus) aggravate food insecurity among small-scale farmers. Host plant resistance is a method of LGB control which should be prioritized in order to reduce these losses. The objective of this study was to assess maize resistance to the larger grain borer and recognize some potential causes of resistance. One hundred and sixty-three (163) genotypes were tested; these included 85 hybrids, 2 checks, 6 open pollinate varieties, and 70 landraces, among them gene bank accessions. Grain biochemical content, (protein, oil and starch) and insect resistance parameters, (percentage grain damage, weight loss, flour weight, and number of emerged insects) were measured. There were significant differences (P < 0.001) among the genotypes for all the traits measured except number of insects. The most resistant hybrids were CKPH08024, CKPH08009, CKPH08012, CKPH08014, CKP08033, CKPH08026, CKPH08014, and CKPH08003. The most resistant landrace accessions were BRAZ 2451, GUAT 1162, BRAZ 2100, and GUAN 36. The percentage weight loss was found to be the most important resistance trait for discriminating among genotypes for it had the largest canonical coefficient. Protein content had higher contribution to variation in resistance to the larger grain borer and this probably contributed to the grain hardness which is a putative trait of resistance to storage pests. The LGB-resistant germplasm could be used for the development of an integrated pest-management program against the LGB.

Published in BMC Genomics  13 : 113, 2012

Kassa Semagn, Cosmos Magorokosho, Bindiganavile S. Vivek, Dan Makumbi, Yoseph Beyene, Stephen Mugo, B. M. Prasanna and Marilyn L. Warburton

Knowledge of germplasm diversity and relationships among elite breeding materials   is fundamentally important in crop improvement. We genotyped 450 maize inbred lines   developed and/or widely used by CIMMYT breeding programs in both Kenya and Zimbabwe   using 1065 SNP markers to (i) investigate population structure and patterns of relationship   of the germplasm for better exploitation in breeding programs; (ii) assess the usefulness   of SNPs for identifying heterotic groups commonly used by CIMMYT breeding programs;   and (iii) identify a subset of highly informative SNP markers for routine and low   cost genotyping of CIMMYT germplasm in the region.

Published in Crop Science  52 (3): 1235-1245, 2012

Lewis Machida, John Derera, Pangirayi Tongoona, Onisimo Mutanga and John MacRobert

Nutritional advantages of quality protein maize (QPM) (Zea mays L.) over normal endosperm maize (NM) were previously demonstrated by several researchers. However, QPM grain quality loss occurs when a QPM crop receives pollen from NM. This is because the opaque-2 gene allele that confers the QPM trait is recessive. The objective was to estimate outcrossing levels and patterns in QPM growing adjacent to NM. White grain QPM crops were grown on nine blocks of 0.21 ha each surrounded by at least a 10-m band of yellow NM at two sites in Zimbabwe. At maturity 160 samples of five QPM ears each were randomly selected to determine outcrossing. Outcrossing was estimated as percentage of yellow kernels on each ear. Ordinary kriging was used to estimate outcrossing levels in areas that were not sampled. Both prediction and error surfaces were produced for each block using the best ordinary kriging model out of the available 11 in ArcMAP 9.2 computer package. Results indicated that five models (exponential, stable, pentaspherical, rational quadratic, and J-Bessel) predicted outcrossing patterns of the nine experiments. Outcrossing levels were high (63 to 83%) in the peripheral areas of the QPM crops, but less than 20% outcrossing was observed on at least 60% of each of the crop areas with no significant compromise of QPM quality based on a QPM quality index of 0.8. In conclusion, QPM and NM can coexist, and ordinary kriging could be used in visualizing spatial distribution of outcrossing in a QPM crop.

Published in Crop Science  52 (3): 1123-1131, 2012

M. S. Lopes, M. P. Reynolds, Y. Manes, R. P. Singh, J. Crossa and H. J. Braun

The genetic yield progress of 26 spring wheat (Triticum aestivum L.) advanced lines released by the International Maize and Wheat Improvement Centre (CIMMYT) in the period from 1977 to 2008 was evaluated in the selection environment in Mexico as well as at a set of target environments in Asia and Africa. In Mexico, grain yield progress was significantly linear and about 0.7% yr⁻¹ and yield was associated with fewer days to heading, cooler canopy temperature at grain filling, and increased stay-green and thousand kernel weight. These results suggested that changes in the former traits at least partially explain the yield progress. When genetic yield progress was measured in subsets of sites in Asia and Africa grouped into high, intermediate, and low yielding, the genetic yield progress was 0.9, 0.7, and 0.5% yr⁻¹, respectively. We conclude that there is no evidence that genetic gains to increase yield have slowed down in wheat lines released by CIMMYT.

Published in Field Crops Research  132 : 175-184, 2012

Diego Valbuena, Olaf Erenstein, Sabine Homann-Kee Tui, Tahirou Abdoulaye, Lieven Claessens, Alan J. Duncan, Bruno Gerard,  Mariana C. Rufino, Nils Teufel, André van Rooyen, Mark T. van Wijk

Conservation Agriculture (CA) is being advocated to enhance soil health and sustain long term crop productivity in the developing world. One of CA’s key principles is the maintenance of soil cover often by retaining a proportion of crop residues on the field as mulch. Yet smallholder crop–livestock systems across Africa and Asia face trade-offs among various options for crop residue use. Knowledge of the potential trade-offs of leaving more residues as mulch is only partial and the objective of this research is to address some of these knowledge gaps by assessing the trade-offs in contrasting settings with mixed crop–livestock systems. The paper draws from village surveys in 12 sites in 9 different countries across Sub-Sahara Africa and South Asia. Sites were clustered into 3 groups along the combined population and livestock density gradients to assess current crop residue management practices and explore potential challenges to adopting mulching practices in different circumstances. Results show that although high-density sites face higher potential pressure on resources on an area basis, biomass production tends to be more substantial in these sites covering demands for livestock feed and allowing part of the residues to be used as mulch. In medium-density sites, although population and livestock densities are relatively lower, biomass is scarce and pressure on land and feed are high, increasing the pressure on crop residues and their opportunity cost as mulch. In low-density areas, population and livestock densities are relatively low and communal feed and fuel resources exist, resulting in lower potential pressure on residues on an area basis. Yet, biomass production is low and farmers largely rely on crop residues to feed livestock during the long dry season, implying substantial opportunity costs to their use as mulch. Despite its potential benefit for smallholder farmers across the density gradient, the introduction of CA-based mulching practices appears potentially easier in sites where biomass production is high enough to fulfil existing demands for feed and fuel. In sites with relatively high feed and fuel pressure, the eventual introduction of CA needs complementary research and development efforts to increase biomass production and/or develop alternative sources to alleviate the opportunity costs of leaving some crop residues as mulch.

Published in Journal of Development and Agricultural Economics  4 (7): 199-209, 2012

Moti Jaleta and Berhanu Gebremedhin

Using simultaneous-equation models, this paper examines whether there is interdependence between smallholder’s net market positions in crop and live animal markets under mixed crop-livestock system. Household level data collected in 2009 from 1075 sample households in 10 districts of Ethiopia are used for this analysis. Results confirmed the existence of interdependence between household’s net positions in crop and live animals markets and relatively, the net position of households in the live animal market is more strongly affected by their net position in the crop market than vice versa. The interdependence between the two market positions showed that households stock live animal asset through selling of surplus crops produced and finance crop purchased through livestock sales. The relatively strong effect of net position in crop market in explaining household’s net positions in live animal market shows the extent of household’s reliance on its position in the crop market while dealing with its participation in live animal market. Thus, policies/strategies enhancing smallholders’ participation in crop and live animal markets in mixed crop-livestock system should pay attention to the production and marketing of both commodities simultaneously.

Published in Weed Science   60 (2): 283-289, 2012

Joel Ransom, Fred Kanampiu, Jonathan Gressel, Hugo De Groote, Michael Burnet and George Odhiambo

Striga is a major constraint to food production in Africa. Most technologies developed for the eradication of Striga asiatica from the United States are not adaptable to Africa. Imazapyr and pyrithiobac coated imidazolinone-resistant (IR)-resistant maize seed prior to planting at rates of 30 to 45 g ha⁻¹ provide near season long control of Striga and can increase maize yields three- to fourfold if supplied with fertilizer. Slow release seed coatings reduce maize injury when post-planting rains are sparse and improve Striga control when there is excessive rainfall early in the season. Models suggest that herbicide resistance may not be a significant threat in short season maize, but vigilance in removing flowering Striga plants that are not controlled is recommended due to the known risk of evolution of resistance to these herbicides. Stacking the IR gene with glyphosate resistance and using imazapyr treated seed and applying glyphosate mid-season would provide season long Striga control and delay the evolution of resistance to both herbicides. To date, adoption of this technology has been limited by a number of factors. However, it should be included as one component of a multi-factor approach to increasing maize productivity in areas of Africa where Striga is problematic.