Genomic prediction models for grain yield of spring bread wheat in diverse agro-ecological zones : Scientific Reports

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Genomic and pedigree predictions for grain yield and agronomic traits were carried out using high density molecular data on a set of 803 spring wheat lines that were evaluated in 5 sites characterized by several environmental co-variables. Seven statistical models were tested using two random cross-validations schemes. Two other prediction problems were studied, namely predicting the lines’ performance at one site with another (pairwise-site) and at untested sites (leave-one-site-out). Grain yield ranged from 3.7 to 9.0 t ha−1across sites. The best predictability was observed when genotypic and pedigree data were included in the models and their interaction with sites and the environmental co-variables. The leave-one-site-out increased average prediction accuracy over pairwise-site for all the traits, specifically from 0.27 to 0.36 for grain yield. Days to anthesis, maturity, and plant height predictions had high heritability and gave the highest accuracy for prediction models. Genomic and pedigree models coupled with environmental co-variables gave high prediction accuracy due to high genetic correlation between sites. This study provides an example of model prediction considering climate data along-with genomic and pedigree information. Such comprehensive models can be used to achieve rapid enhancement of wheat yield enhancement in current and future climate change scenario.

Source: Genomic prediction models for grain yield of spring bread wheat in diverse agro-ecological zones : Scientific Reports

High-Provitamin A Carotenoid (Orange) Maize Increases Hepatic Vitamin A Reserves of Offspring in a Vitamin A-Depleted Sow-Piglet Model during Lactation

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The relationship of dietary vitamin A transfer from mother to fetus is not well understood. The difference in swine offspring liver reserves was investigated between single-dose vitamin A provided to the mother post-conception compared with continuous provitamin A carotenoid dietary intake from biofortified (enhanced provitamin A) orange maize (OM) fed during gestation and lactation. Vitamin A-depleted sows were fed OM (n = 5) or white maize (WM) + 1.05 mmol retinyl palmitate administered at the beginning of gestation (n = 6). Piglets (n = 102) were killed at 0, 10, 20, and 28 d after birth. Piglets from sows fed OM had higher liver retinol reserves (P < 0.0001) and a combined mean concentration from d 10 to 28 of 0.11 ± 0.030 μmol/g. Piglets from sows fed WM had higher serum retinol concentrations (0.56 ± 0.25 μmol/L; P = 0.0098) despite lower liver retinol concentrations of 0.068 ± 0.026 μmol/g from d 10 to 28. Milk was collected at 0, 5, 10, 20, and 28 d. Sows fed OM had a higher milk retinol concentration (1.36 ± 1.30 μmol/L; P = 0.038), than those fed WM (0.93 ±1.03 μmol/L). Sow livers were collected at the end of the study (n = 3/group) and had identical retinol concentrations (0.22 ± 0.05 μmol/g). Consumption of daily provitamin A carotenoids by sows during gestation and lactation increased liver retinol status in weanling piglets, illustrating the potential for provitamin A carotenoid consumption from biofortified staple foods to improve vitamin A reserves. Biofortified OM could have a measurable impact on vitamin A status in deficient populations if widely adopted.

Source: High-Provitamin A Carotenoid (Orange) Maize Increases Hepatic Vitamin A Reserves of Offspring in a Vitamin A-Depleted Sow-Piglet Model during Lactation

Mapping of spot blotch disease resistance using NDVI as a substitute to visual observation in wheat (Triticumaestivum L.)

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Evaluation of wheat for spot blotch disease resistance relies on various visual observation methods. The person evaluating the lines needs to be experienced in scoring disease severity. To facilitate

Source: Mapping of spot blotch disease resistance using NDVI as a substitute to visual observation in wheat (Triticumaestivum L.) | SpringerLink

Different QTLs are associated with leaf rust resistance in wheat between China and Mexico

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The wheat line ‘Chapio’ is resistant to leaf rust, caused by Puccinia triticinia, and was derived from a breeding programme that focuses on multi-genic resistance to provide durability. This line was crossed with the susceptible ‘Avocet’ to develop an F6 recombinant inbred line population. The population was phenotyped for leaf rust severity in two environments each in Mexico and China. There were significant differences in the loci providing resistance between the two intercontinental regions. The Lr34 locus had large effects in both Mexico and China, highlighting its importance in providing a basis for broad-spectrum resistance. The Lr46 locus on chromosome 1BL and a 3D locus had effects in Mexico but not in China. Presence of Sr2 was determined by the phenotypic marker of pseudo-black chaff and was mapped to chromosome 3BS. This region was associated with a QTL that had strong effects in China but no significant effect in Mexico, as did a locus on chromosome 4B. Seedling tests on the parents indicated that the 3B locus was not the complimentary gene Lr27, but the 4B locus was in the same position as Lr31 (or Lr12). Further investigations showed that these loci worked independently and additively in adult plants. Chapio was bred for quantitative, non-race-specific resistance under strong phenotypic selection for leaf rust in Mexico. It is interesting that different QTLs contribute to this resistance in another country, and these results suggest that environmental effects, as well as race specificity, can play a role in expression of resistance.

Source: Koha online catalog › Details for: Different QTLs are associated with leaf rust resistance in wheat between China and Mexico

Mining centuries old In situ conserved turkish wheat landraces for grain yield and stripe rust resistance genes

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58094Authors: Sehgal, D.; Dreisigacker, S.; Belen, S.; Kucukozdemir, U.; Mert, Z.; Ozer, E.; Morgounov, A.I.

Published in: Frontiers in genetics, 2016, vol.7, no.201.


Wheat landraces in Turkey are an important genetic resource for wheat improvement. An exhaustive 5-year (2009–2014) effort made by the International Winter Wheat Improvement Programme (IWWIP), a cooperative program between the Ministry of Food, Agriculture and Livestock of Turkey, the International Center for Maize and Wheat Improvement (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA), led to the collection and documentation of around 2000 landrace populations from 55 provinces throughout Turkey. This study reports the genetic characterization of a subset of bread wheat landraces collected in 2010 from 11 diverse provinces using genotyping-by-sequencing (GBS) technology. The potential of this collection to identify loci determining grain yield and stripe rust resistance via genome-wide association (GWA) analysis was explored. A high genetic diversity (diversity index = 0.260) and a moderate population structure based on highly inherited spike traits was revealed in the panel. The linkage disequilibrium decayed at 10 cM across the whole genome and was slower as compared to other landrace collections. In addition to previously reported QTL, GWA analysis also identified new candidate genomic regions for stripe rust resistance, grain yield, and spike productivity components. New candidate genomic regions reflect the potential of this landrace collection to further increase genetic diversity in elite germplasm.

Africa’s changing farm size distribution patterns : the rise of medium-scale farms

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58096Authors: Jayne, T.S., Chamberlin, J.; Traub, L.; Sitko, N.J.; Muyanga, M.; Yeboah, K.; Anseeuw, W.; Chapoto, A.; Ayala Wineman; Nkonde, C.; Kachule, R.

Published in: Agricultural Economics, 2016, vol. 47 (supplement), p. 197-214


Mexico is the center of origin of diversification of maize (Zea mays L.), there are 3.2 million corn growers and is the largest crop harvested. Most of these producers are in the rural sector, in poverty and inequality. Despite this genetic diversity and represent about 65% of the cultivated area it is little attention has been given to the potential of native maize in commercial terms. The marketing of landraces can be carried out in traditional local markets and specialty markets. This research aimed to identify the dynamics of actual marketing of native maize in Mexico in order to identify options trading in specialty markets for the conservation of the biodiversity of these corns and improve the income of producers. The 492 interviews were made with farmers, traders and processors of native maize customers in the states of Mexico, Tlaxcala and Guerrero. The results show that the main specialty corns produced are the colors and within these the most important in marketing are the targets by consumer preferences corns. It is concluded that currently the market is landraces in traditional local markets; however there is potential for the development of specialty markets that require value added.

The geography of Zambia’s customary land : assessing the prospects for smallholder development

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57950Authors: Sitko, N.J. and Chamberlin, J.

Published in: Land Use Policy, 2016, vol.55, p.49-60


This article utilizes available spatial data to quantify the amount of customary land in Zambia and to examine the prospects for agricultural commercialization in those areas, in terms of population densities, market access conditions, and agro-ecological suitability. We find that approximately 51–54 percent of Zambia’s land remains under customary tenure and, by implication, available for smallholder utilization. However, populations are clustered in 5 percent of the customary land with reasonably good market access conditions. Good market access conditions are generally located in regions with high levels of rainfall variability due to historical infrastructure investments. High density, market accessible regions are witnessing a rapid increase in land commodification, land alienation, and declining fallow rates. Land and economic development policies must be attentive to the changing dynamics in customary land areas in order to ensure the future viability of the smallholder farming sector.

Crop residue allocation to livestock feed, soil improvement and other uses along a productivity gradient in Eastern Africa

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57951Author(s): Duncan, A.J.; Bachewe, F.; Mekonnen, K.; Valbuena, D.; Rachier, G.; Lule, D.; Bahta, M.; Erenstein, O.

Published in: Agriculture, Ecosystems and Environment 2016, vol.228, p.101-110


Crop residues are a key livelihood resource in smallholder mixed crop-livestock systems in Sub-Saharan Africa. With expansion of arable land and resultant decline in grazing resources, crop residues are becoming an increasingly important component of livestock feeds. This demand for livestock feeds has implications for the long-term sustainability of such systems since failure to return biomass to soils has implications for soil quality and the capacity of soils to support long-term productivity. Biomass allocation patterns are likely to vary with overall level of productivity and hence availability. In this study we used a household survey to quantify crop residue allocation patterns across a gradient of productivity in Eastern Africa focusing on two sites in Ethiopia and one in Kenya. We assessed the underlying determinants of crop residue allocation patterns with a view to understanding how productivity increases through intensification will influence biomass allocation in Eastern Africa and how livelihood and natural resource management objectives could be optimized. Results showed that farmers strongly favour allocation of residues to livestock feeding but that allocation to soil increases along the productivity gradient. This reduced feeding to livestock and increased allocation to soil fertility is associated with smaller farm sizes leading to reduced animal traction needs for tillage, increased overall livestock productivity, increased use of inputs and a reduced reliance on farm-based activities in overall livelihood strategies. The implications of these trends are that productivity increases in smallholder systems are likely to reduce pressure on biomass in the long term and that measures that enhance the prospects for farmers to intensify their production systems are likely to increase soil health and sustainability objectives in general. A key conclusion of the work is that intensification of livestock production could reduce crop residue allocation to soils with long term implications for soil productivity.

The development of quality control genotyping approaches : a case study using elite maize lines

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57954Authors: Jiafa Chen.; Zavala, C.; Ortega, N.; Petroli, C.D.; Franco-Barrera, J.; Burgueño, J.; Costich, D.E.; Hearne, S.

Published in: PLoS One 2016, vol.11, no.6: e0157236


Quality control (QC) of germplasmidentity and purity is a critical component of breeding and conservation activities. SNP genotyping technologies and increased availability of markers provide the opportunity to employ genotyping as a low-cost and robust component of this QC. In the public sector available low-cost SNP QC genotypingmethods have been developed from a very limited panel ofmarkers of 1,000 to 1,500 markers without broad selection of the most informative SNPs. Selection of optimal SNPs and definition of appropriate germplasm sampling in addition to platform section impact on logistical and resource-use considerations for breeding and conservation applications when mainstreaming QC. In order to address
these issues, we evaluated the selection and use of SNPs for QC applications from large DArTSeq data sets generated from CIMMYT maize inbred lines (CMLs). Two QC genotyping strategies were developed, the first is a “rapid QC”, employing a small number of SNPs to identify potential mislabeling of seed packages or plots, the second is a “broad QC”, employing a larger number of SNP, used to identify each germplasm entry and tomeasure heterogeneity. The optimal marker selection strategies combined the selection ofmarkers with high minor allele frequency, sampling of clustered SNP in proportion tomarker cluster distance and selecting markers thatmaintain a uniform genomic distribution. The rapid and broad QC SNP panels selected using this approach were further validated using blind test assessments of related re-generation samples. The influence of sampling within each line was evaluated. Sampling 192 individuals would result in close to 100% possibility of detecting a 5%contamination in the entry, and approximately a 98%probability to detect a 2%contamination of the line. These results provide a framework for the establishment of QC genotyping. A comparison of financial and time costs for use of these approaches across different platforms is discussed providing a framework for institutions involved inmaize conservation and breeding to assess the resource use effectiveness of QC genotyping. Application of these research findings, in combination with existing QC approaches, will ensure the regeneration, distribution and use in breeding of true to type inbred germplasm. These findings also provide an effective approach to optimize SNP selection for QC genotyping in other species.

Effects of relay cover crop planting date on their biomass and maize productivity in a sub-humid region of Zimbabwe under conservation agriculture

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57955Authors: Mhlanga, B.; Cheesman, S.; Maasdorp, B.; Mupangwa, W.; Munyoro, C.; Sithole, C.; Thierfelder, C.

Published in: NJAS Wageningen Journal of Life Sciences, 2016, vol.78, p.93–101.


Relay cropping of cover crops is a strategy of increasing biomass yields and productivity of maize-based systems. However, there is need to strategically plan the relay cropping to avoid competition between the main crop and the relay cover crops while at the same time obtaining optimum yields from both crops. A study was carried out in a clay soil in a sub-humid region of Zimbabwe to investigate the effect of introducing different relay cover crops at 8, 11 and 15 weeks after planting maize (WAPM) into a standing maize crop on biomass yield of the relay cover crops, their emergence and maize yields in the 2012–13 and 2013–14 seasons. From the results of the study, it was observed that the introduction of relay cover crops late in the season compromises their emergence and hence biomass yields (as low as 0.8 kg ha−1 for blue lupins (Lupinus angustifolius var. angustifolius (L.)). In a season where longer mid-season dry spells were experienced (2013–14), biomass yields of the relay cover crops were lower than in 2012–13 season. Delays in planting of relay cover crops (i.e. from 8 to 11 and from 11 to 15 WAPM) resulted in yield reductions of around 50%. Relay cover crops introduced at different periods of the season had no significant effects on maize grain and biomass yields. However, there are relay cover crops such as the velvet bean (Mucuna pruriens (L.) DC) and common oats (Avena sativa L.) that showed better emergence even in the sub-optimal conditions (with emergence as high as 90%). Of all the investigated relay cover crops, none could contribute to significant amounts of biomass thus insignificant increases in total plot biomass. There is need to investigate on other earlier planting dates that do not compromise the biomass productivity of such relay cover crops.