Author Archive

Identification of candidate genes for drought tolerance by whole-genome resequencing in maize

Posted by Carelia Juarez on , in Journal Articles

Published in BMC Plant Biology 14 15 p, 2014.

Jie Xu; Yibing Yuan; Yunbi Xu; Gengyun Zhang; Xiaosen Guo; Fengkai Wu; Qi Wang; Tingzhao Rong; Guangtang Pan; Moju Cao; Qilin Tang; Shibin Gao; Yaxi Liu; Jing Wang; Hai Lan; Yanli Lu

Background: Drought stress is one of the major limiting factors for maize production. With the availability of maize B73 reference genome and whole-genome resequencing of 15 maize inbreds, common variants (CV) and clustering analyses were applied to identify non-synonymous SNPs (nsSNPs) and corresponding candidate genes for drought tolerance. Results: A total of 524 nsSNPs that were associated with 271 candidate genes involved in plant hormone regulation, carbohydrate and sugar metabolism, signaling molecules regulation, redox reaction and acclimation of photosynthesis to environment were detected by CV and cluster analyses. Most of the nsSNPs identified were clustered in bin 1.07 region that harbored six previously reported QTL with relatively high phenotypic variation explained for drought tolerance. Genes Ontology (GO) analysis of candidate genes revealed that there were 35 GO terms related to biotic stimulus and membrane-bounded organelle, showing significant differences between the candidate genes and the reference B73 background. Changes of expression level in these candidate genes for drought tolerance were detected using RNA sequencing for fertilized ovary, basal leaf meristem tissue and roots collected under drought stressed and well-watered conditions. The results indicated that 70% of candidate genes showed significantly expression changes under two water treatments and our strategies for mining candidate genes are feasible and relatively efficient. Conclusions: Our results successfully revealed candidate nsSNPs and associated genes for drought tolerance by comparative sequence analysis of 16 maize inbred lines. Both methods we applied were proved to be efficient for identifying candidate genes for complex traits through the next-generation sequencing technologies (NGS). These selected genes will not only facilitate understanding of genetic basis of drought stress response, but also accelerate genetic improvement through marker-assisted selection in maize.

Meta-analysis and candidate gene mining of low-phosphorus tolerance in maize

Posted by Carelia Juarez on , in Journal Articles

Published in Journal of Integrative Plant Biology 56 (3262-270, 2014.

Hongwei Zhang; Uddin, M.S.;Cheng Zou; Chuanxiao Xie; Yunbi Xu; Wen-Xue Li

Plants with tolerance to low-phosphorus (P) can grow better under low-P conditions, and understanding of genetic mechanisms of low-P tolerance can not only facilitate identifying relevant genes but also help to develop low-P tolerant cultivars. QTL meta-analysis was conducted after a comprehensive review of the reports on QTL mapping for low-P tolerance-related traits in maize. Meta-analysis produced 23 consensus QTL (cQTL), 17 of which located in similar chromosome regions to those previously reported to influence root traits. Meanwhile, candidate gene mining yielded 215 genes, 22 of which located in the cQTL regions. These 22 genes are homologous to 14 functionally characterized genes that were found to participate in plant low-P tolerance, including genes encoding miR399s, Pi transporters and purple acid phosphatases. Four cQTL loci (cQTL2-1, cQTL5-3, cQTL6-2, and cQTL10-2) may play important roles for low-P tolerance because each contains more original QTL and has better consistency across previous reports.

Kernel number as a positive target trait for prediction of hybrid performance under low-nitrogen stress as revealed by diallel analysis under contrasting nitrogen conditions

Posted by Carelia Juarez on , in Journal Articles

Published in Breeding Science 64 389-398, 2014

Xiuxiu Li; Zhen Sun; Xiaojie Xu; Wen-Xue Li; Cheng Zou;Shanhong Wang; Yunbi Xu; Chuanxiao Xie

Environmental sustainability concerns make improving yield under lower N input a desirable breeding goal. To evaluate genetic variation and heterosis for low-N tolerance breeding, 28 F1 hybrids from a diallel scheme, along with their eight parental lines, were tested for agronomic traits including kernel number per ear (KNE) and grain yield per plant (GY), in replicated plots over two years under low-nitrogen (LN, without nitrogen application) and normal-nitrogen (NN, 220 kg N ha–1) conditions. Taken together the heritability in this and our previous studies, the correlation with grain yield, and the sensitivity to the stress for target trait selection, KNE was a good secondary target trait for LN selection in maize breeding. KNE also showed much higher mid-parent heterosis than hundred-kernel weight under both nitrogen levels, particularly under LN, indicating that KNE contributed the majority of GY heterosis, particularly under LN. Therefore, KNE can be used as a positive target trait for hybrid performance prediction in LN tolerance breeding. Our results also suggest that breeding hybrids for LN tolerance largely relies on phenotypic evaluation of hybrids under LN condition and yield under LN might be improved more by selection for KNE than by direct selection for GY per se.

Higher flower and seed number leads to higher yield under water stress conditions imposed during reproduction in chickpea

Posted by Carelia Juarez on , in Journal Articles

Published in Functional Plant Biology42(2):162-174, 2014.

Pushpavalli, R.; Zaman-Allah, M.; Turner, N.C.; Baddam, R.; Rao, M.V.; Vadez, V.

The reproductive phase of chickpea (Cicer arietinum L.) is more sensitive to water deficits than the vegetative phase. The characteristics that confer drought tolerance to genotypes at the reproductive stage are not well understood; especially which characteristics are responsible for differences in seed yield under water stress. In two consecutive years, 10 genotypes with contrasting yields under terminal drought stress in the field were exposed to a gradual, but similar, water stress in the glasshouse. Flower number, flower + pod + seed abortion percentage, pod number, pod weight, seed number, seed yield, 100-seed weight (seed size), stem + leaf weight and harvest index (HI) were recorded in well watered plants (WW) and in water-stressed plants (WS) when the level of deficit was mild (phase I), and when the stress was severe (phase II). The WS treatment reduced seed yield, seed and pod number, but not flower + pod + seed abortion percentage or 100-seed weight. Although there were significant differences in total seed yield among the genotypes, the ranking of the seed yield in the glasshouse differed from the ranking in the field, indicating large genotype × environment interaction. Genetic variation for seed yield and seed yield components was observed in the WW treatment, which also showed differences across years, as well as in the WS treatment in both the years, so that the relative seed yield and relative yield components (ratio of values under WS to those under WW) were used as measures of drought tolerance. Relative total seed yield was positively associated with relative total flower number (R2 = 0.23 in year 2) and relative total seed number (R2 = 0.83, R2 = 0.79 in years 1 and 2 respectively). In phase I (mild stress), relative yield of seed produced in that phase was found to be associated with the flower number in both the years (R2 = 0.69, R2 = 0.76 respectively). Therefore, the controlled drought imposition that was used, where daily water loss from the soil was made equal for all plants, revealed genotypic differences in the sensitivity of the reproductive process to drought. Under these conditions, the seed yield differences in chickpea were largely related to the capacity to produce a large number of flowers and to set seeds, especially in the early phase of drought stress when the degree of water deficit was mild.

Enhancing laccase production by a newly-isolated strain of Pycnoporus sanguineus with high potential for dye decolouration

Posted by Carelia Juarez on , in Journal Articles

Published in RSC Advances 64 34096-34103, 2014.

Gioia, L.; Manta, C.; Ovsejevi, K.; Burgueño, J.; Menendeza, P.; Rodriguez-Couto, S.

Response surface methodology (RSM) was applied to optimise laccase production by a new strain of Pycnoporus sanguineus, isolated from the Uruguayan forests, grown on bark shavings under semi-solid-state fermentation conditions. Enhancement of laccase production was studied, with a full 24 factorial design with two replicates and four central points. Operating under the optimal conditions obtained (pH 3.0, yeast extract 10 g L−1, glucose 5 g L−1 and bark shavings 3 g), a laccase activity of nearly 3000 U L−1 was achieved. Subsequently, the effect of different potential inducers on laccase production (Cu+2, Mn+2 and lignin) was tested using the one-factor-at-a-time approach. It was found that the addition of 0.5 mM Cu+2 into the cultures considerably increased laccase production and, thus, maximum activity values of about 16 000 U L−1 were achieved. Further, the optimised culture broth (containing mainly laccase) showed high capacity to decolourise different recalcitrant synthetic dyes such as Acid Red 88 (AR88), Reactive Black 5 (RB5) and Lanaset Grey G (LG). After selecting enzyme concentration and time of reaction, almost 70% of AR88 could be decolourised in the absence of redox mediators. However, mediators were necessary to bleach RB5 and LG. Methyl syringate was the most effective mediator for AR88 (reaching a decolouration degree over 90%) and RB5 (nearly 70%). Around 80% of LG could be decolourised in the presence of violuric acid. These promising results make this enzyme a very useful tool for developing wastewater treatments.

Genetic and molecular bases of yield-associated traits: a translational biology approach between rice and wheat

Posted by Carelia Juarez on , in Journal Articles

Published in Theoretical and Applied Genetics 127 (71463-1489, 2014

Valluru, R.; Reynolds, M.P.; Salse, S.

Transferring the knowledge bases between related species may assist in enlarging the yield potential of crop plants. Being cereals, rice and wheat share a high level of gene conservation; however, they differ at metabolic levels as a part of the environmental adaptation resulting in different yield capacities. This review focuses on the current understanding of genetic and molecular regulation of yield-associated traits in both crop species, highlights the similarities and differences and presents the putative knowledge gaps. We focus on the traits associated with phenology, photosynthesis, and assimilate partitioning and lodging resistance; the most important drivers of yield potential. Currently, there are large knowledge gaps in the genetic and molecular control of such major biological processes that can be filled in a translational biology approach in transferring genomics and genetics informations between rice and wheat.

AlphaMPSim: flexible simulation of multi-parent crosses

Posted by Carelia Juarez on , in Journal Articles

Published in Bioinformatics 30 (182686-2688, 2014.

Hickey, J.M.; Gorjanc, G.; Hearne, S.; Huang, B.E.

Multi-parent crosses of recombinant inbred lines (RILs) exist in many species for fine-scale analysis of genome structure and marker-trait association. These populations encompass a wide range of crossing designs with varying potential. AlphaMPSim is a flexible simulation program that is efficiently designed for comparison of alternative designs for traits with varying genetic architectures and biallelic markers with densities up to full sequence. A large pool of founder haplotypes can be supplied by the user, or generated via integration with external coalescent simulation programs such as MaCS. From these, diverse founders for multi-parent designs can be generated automatically, and users can compare designs generated from diverse pedigrees. Full tracking of identity by descent (IBD) status of alleles within the pedigree is undertaken and output files are compatible with commonly available analysis packages in R.

Designing sustainable agricultural production systems for a changing world: Methods and applications

Posted by Carelia Juarez on , in Journal Articles

Published in Agricultural Systems 126 1-2, 2014

Digliotti, S.; Rodriguez, D.; Lopez-Ridaura, S.; Tittonell, P.; Rossing, W.A.H.

Over the next 40 years agriculture will have to increase food production by an estimated 70% at least, on nearly the same area of land, under increasing costs of energy and other inputs, and under evident climate change (Lobell et al., 2009; State of Food Insecurity in the World, 2013). Ecological intensification of agricultural production has been proposed as a way forward for agriculture to meet these challenges (Cassman, 1999 and Doré et al., 2011). The required practices, technologies, tactics and strategies are likely to differ between low and high income countries, across agro-ecologies, farming systems, and households having access to contrasting levels of resources and markets. It is clear that no single solution will be able to achieve sustainable economic development across this diversity of more or less rural-based economies around the globe. Despite the complexity of the problem, opportunities are urgently needed to increase agricultural production and feed a growing population while reducing the negative environmental impacts of agriculture, and increasing its contribution to natural capital and environmental services.

Developing local adaptation strategies for climate change in agriculture: a priority-setting approach with application to Latin America

Posted by Carelia Juarez on , in Journal Articles

Published in Global Environmental Change 29:78-91, 2014.

Lee, D.R.; Edmeades, S.; De Nys, E.; McDonald, A.; Janssen, W.

Even with substantially increased attention to climate adaptation in developing countries in recent years, there are a number of important remaining research needs: better incorporating stakeholder input; using replicable methodologies to provide comparability across different settings; assuring that stakeholder input reflects the results of climate science, not simply perceptions; and effectively linking stakeholder input with the regional and national levels at which policy changes are made. This study reports the results of a methodology for identifying and prioritizing local, stakeholder-driven response options to climate change in agriculture. The approach is based on multi-criteria scoring methods previously applied to research planning and priority-setting in agricultural and natural resource management research, public health, and other areas. The methodology is a sequential approach built around needs assessments by local stakeholders; the incorporation of climate science results; the sharing of these results and climate adaption response options with stakeholders at a series of workshops; stakeholder priority-setting exercises using multi-criteria scoring; and validation with policymakers. The application is to three diverse agroecosystems in Mexico, Peru and Uruguay. Among the many findings is that, notwithstanding the wide diversity of agro-ecosystems, there are numerous similarities in the agricultural adaptation responses prioritized by local stakeholders.

Rural livelihood diversification strategies in Nepal

Posted by Carelia Juarez on , in Journal Articles

Published in Poverty and Public Policy (3259-281, 2014.

Dil Bahadur Rahut; Ali, A.; Kassie, M.; Marenya, P.; Basnet, C.

This article constructs a rural livelihood strategy using the Nepal Living Standard Survey Measurement from 1996 and 2004 and explores the determinants of rural livelihood strategies. This study finds that education, ethnicity, and location play an important role in livelihood diversification outside agriculture, and suggests the importance of keeping children in school for non-farm livelihood diversification and poverty reduction. Important policy implications of the current study include the need for investment in education, as the current literacy rate in Nepal is quite low. Investing in education will help households to diversify their livelihood outside of the farm and pave a way out of poverty.