Author Archive

Germinate 3 : development of a common platform to support the distribution of experimental data on crop wild relatives

Posted by gabrielamartinez on , in Journal Articles

Conservation and exploitation of crop wild relative species is an important component in ensuring food security and improving current agricultural output. By identifying agriculturally important characteristics that express favorable response to both biotic and abiotic stress currently unused by breeders, the incorporation of this new genetic material into genetic background stocks may help mitigate problems imposed by climate change, land degradation, and population pressure. This is particularly important in countries that will be more severely affected by the threat of reduced yields. The ability to effectively manage genetic resources collections and integrate unique and diverse data types is crucial in exploring, understanding, and exploiting the diversity contained within genebanks. Providing a common interface through which experimental and background data can be disseminated to both researchers and breeders will bring focus and facilitate community building into research communities. We have taken wild barley (Hordeum spp.) and potato (Solanum spp.) collections along with wheat (Triticum spp.) and maize (Zea mays subsp. mays) and their wild relatives and incorporated this data into web-based information resources built using the Germinate platform (https://ics.hutton.ac.uk/get-germinate, accessed 4 Apr. 2017). We have tailored these to better meet the demands of researchers by developing both new data visualization tools and integration with current software such as Helium, Flapjack, and CurlyWhirly (https://ics.hutton.ac.uk/software, accessed 4 Apr. 2017) and presented the data in a common platform. While the underlying species differ, the approach taken ensures that tools are compatible across all database instances. We will describe these database instances and show that Germinate offers a common platform that will aid in the exploration and wider use of these species.

Source: Crop Science v. 57, p.1-15

How can we improve crop genotypes to increase stress resilience and productivity in a future climate? A new crop screening method based on productivity and resistance to abiotic stress

Posted by gabrielamartinez on , in Journal Articles

The need to accelerate the selection of crop genotypes that are both resistant to and productive under abiotic stress is enhanced by global warming and the increase in demand for food by a growing world population. In this paper, we propose a new method for evaluation of wheat genotypes in terms of their resilience to stress and their production capacity. The method quantifies the components of a new index related to yield under abiotic stress based on previously developed stress indices, namely the stress susceptibility index, the stress tolerance index, the mean production index, the geometric mean production index, and the tolerance index, which were created originally to evaluate drought adaptation. The method, based on a scoring scale, offers simple and easy visualization and identification of resilient, productive and/or contrasting genotypes according to grain yield. This new selection method could help breeders and researchers by defining clear and strong criteria to identify genotypes with high resilience and high productivity and provide a clear visualization of contrasts in terms of grain yield production under stress. It is also expected that this methodology will reduce the time required for first selection and the number of first-selected genotypes for further evaluation by breeders and provide a basis for appropriate comparisons of genotypes that would help reveal the biology behind high stress productivity of crops.

Source: Journal of Experimental Botany | Oxford Academic

Identification of Genomic Associations for Adult Plant Resistance in the Background of Popular South Asian Wheat Cultivar, PBW343

Posted by gabrielamartinez on , in Journal Articles

Rusts, a fungal disease as old as its host plant wheat, an enemy as old as wheat, has caused havoc for over 8,000 years. As the rust pathogens can evolve into new virulent races which quickly defeat to qualitative or vertical the resistance that primarily rely on race specificity over time, adult plant resistance (APR) has often been found to be race non-specific and hence is considered have been proven to be a more to be a more reliable and durable strategy to combat this malady. Over decades sets of donor lines have been identified at International Maize and Wheat Improvement Center (CIMMYT) representing a wide range of APR sources in wheat. In this study, using nine donors and a common parent ‘PBW343’, a popular Green Revolution variety at CIMMYT, the nested association mapping (NAM) population of 1122 lines was constructed to understand the APR genetics underlying these founder lines. Thirty-four QTL were associated with APR to rusts, and 20 of 34 QTL had pleiotropic effects on SR, YR and LR resistance. Three chromosomal regions, associated with known APR genes (Sr58/Yr29/Lr46, Sr2/Yr30/Lr27, and Sr57/Yr18/Lr34), were also identified, 13 previously reported QTL regions were validated. Of the 18 QTL first detected in this study, 7 were pleiotropic QTL, distributing on chromosomes 3A, 3B, 6B, 3D, and 6D. The present investigation revealed the genetic relationship of historical APR donor lines, the novel knowledge on APR, as well as the new analytical methodologies to facilitate the applications of NAM design in crop genetics. Results shown in this study will aid the parental selection for hybridization in wheat breeding, and envision the future rust management breeding for addressing potential threat to wheat production and food security.

Source: Frontiers | Identification of Genomic Associations for Adult Plant Resistance in the Background of Popular South Asian Wheat Cultivar, PBW343 | Plant Science

Wheat quality improvement at CIMMYT and the use of genomic selection on it

Posted by gabrielamartinez on , in Journal Articles

The International Center for Maize and Wheat Improvement (CIMMYT) leads the Global Wheat Program, whose main objective is to increase the productivity of wheat cropping systems to reduce poverty in developing countries. The priorities of the program are high grain yield, disease resistance, tolerance to abiotic stresses (drought and heat), and desirable quality. TheWheat Chemistry and Quality Laboratory has been continuously evolving to be able to analyze the largest number of samples possible, in the shortest time, at lowest cost, in order to deliver data on diverse quality traits on time to the breeders formaking selections for advancement in the breeding pipeline. The participation of wheat quality analysis/selection is carried out in two stages of the breeding process: evaluation of the parental
lines for new crosses and advanced lines in preliminary and elite yield trials. Thousands of lines are analyzed which requires a big investment in resources. Genomic selection has been proposed to assist in selecting for quality and other traits in breeding programs. Genomic selection can predict quantitative traits and is applicable to multiple quantitative traits in a breeding pipeline by attaining historical phenotypes and adding high-density genotypic information. Due to advances in sequencing technology, genome-wide single nucleotide polymorphism markers are available through genotyping-by-sequencing at a cost conducive to application for genomic selection. At CIMMYT, genomic selection has been applied to predict all of the processing and end-use quality traits regularly tested in the spring wheat breeding program. These traits have variable levels of prediction accuracy, however, they demonstrated thatmost expensive traits, dough rheology and baking final product, can be predicted with a high degree of confidence. Currently it is being explored howto combine both phenotypic and genomic selection to make more efficient the genetic improvement for quality traits at CIMMYT spring wheat breeding program.

 

Source: Wheat quality improvement at CIMMYT and the use of genomic selection on it

Effect of different mulching materials on maize growth and yield in conservation agriculture systems of sub-humid Zimbabwe

Posted by gabrielamartinez on , in Journal Articles

The introduction of conservation agriculture (CA) for smallholders increased the competition for crop residues between crop and livestock enterprises of the mixed smallholder farming system. Smallholders practicing CA have resorted to using grass and leaf litter in addition to available crop residues. The effect of these different mulching materials on maize (Zea mays L.) growth and yield is not well documented in smallholder CA systems of southern Africa. A two-year experiment was run in 2012/13 and 2013/14 seasons to evaluate the effect of maize residues, grass (Hyparrhenia filipendula (L.) Stapf.) and leaf litter that farmers are currently using and residues from leguminous species, sunhemp (Crotolaria juncea L.) and Tephrosia (Tephrosia vogelii ((Hook) f.)) on maize nitrogen (N) uptake, growth and yield. Significant differences in soil water content across treatments were only observed during March in 2012/13 season. Maize residues retained more soil water and Tephrosia had the lowest soil water content when seasonal rainfall pattern was erratic. Grass and Tephrosia treatments had the lowest chlorophyll content. Conventional ploughing, maize residues and leaf litter had similar chlorophyll content which was significantly higher than grass and Tephrosia treatments. At a site with higher initial soil fertility conventional ploughing treatment out yielded the other treatments by 727–1265 kg ha−1. With more degraded sandy soil conventional practice had 119–430 kg ha−1 more maize grain than the CA treatments. With adequate fertilization, the mulching materials have a similar effect on maize growth in basins and direct seeding. Further studies on different application rates of mulching materials and mineral N fertilizer, and nutrient release patterns of these residues are critical in order to better understand soil fertility management under smallholder CA systems.

Source: Open Access Journals

Identification of Genomic Associations for Adult Plant Resistance in the Background of Popular South Asian Wheat Cultivar, PBW343

Posted by gabrielamartinez on , in Journal Articles

Rusts, a fungal disease as old as its host plant wheat, an enemy as old as wheat, has caused havoc for over 8,000 years. As the rust pathogens can evolve into new virulent races which quickly defeat to qualitative or vertical the resistance that primarily rely on race specificity over time, adult plant resistance (APR) has often been found to be race non-specific and hence is considered have been proven to be a more to be a more reliable and durable strategy to combat this malady. Over decades sets of donor lines have been identified at International Maize and Wheat Improvement Center (CIMMYT) representing a wide range of APR sources in wheat. In this study, using nine donors and a common parent ‘PBW343’, a popular Green Revolution variety at CIMMYT, the nested association mapping (NAM) population of 1122 lines was constructed to understand the APR genetics underlying these founder lines. Thirty-four QTL were associated with APR to rusts, and 20 of 34 QTL had pleiotropic effects on SR, YR and LR resistance. Three chromosomal regions, associated with known APR genes (Sr58/Yr29/Lr46, Sr2/Yr30/Lr27, and Sr57/Yr18/Lr34), were also identified, 13 previously reported QTL regions were validated. Of the 18 QTL first detected in this study, 7 were pleiotropic QTL, distributing on chromosomes 3A, 3B, 6B, 3D, and 6D. The present investigation revealed the genetic relationship of historical APR donor lines, the novel knowledge on APR, as well as the new analytical methodologies to facilitate the applications of NAM design in crop genetics. Results shown in this study will aid the parental selection for hybridization in wheat breeding, and envision the future rust management breeding for addressing potential threat to wheat production and food security.

Source: Frontiers | Identification of Genomic Associations for Adult Plant Resistance in the Background of Popular South Asian Wheat Cultivar, PBW343 | Plant Genetics and Genomics

Modelling and genetic dissection of staygreen under heat stress | SpringerLink

Posted by gabrielamartinez on , in Journal Articles

Plant chlorophyll retention—staygreen—is considered a valuable trait under heat stress. Five experiments with the Seri/Babax wheat mapping population were sown in Mexico under hot-irrigated environments. Normalized difference vegetation index (NDVI) during plant growth was measured regularly and modelled to capture the dynamics of plant greenness decay, including staygreen (Stg) at physiological maturity which was estimated by regression of NDVI during grainfilling. The rate of senescence, the percentage of plant greenness decay, and the area under the curve were also estimated based on NDVI measurements. While Stg and the best fitted curve were highly environment dependent, both traits showed strong (positive for Stg) correlations with yield, grainfilling rates, and extended grainfilling periods, while associations with kernel number and kernel weight were weak. Stg expression was largely dependent on rate of senescence which was related to the pattern of the greenness decay curve and the initial NDVI. QTL analyses revealed a total of 44 loci across environments linked to Stg and related traits, distributed across the genome, with the strongest and most repeatable effects detected on chromosomes 1B, 2A, 2B, 4A, 4B and 7D. Of these, some were common with regions controlling phenology but independent regions were also identified. The co-location of QTL for Stg and performance traits in this study confirms that the staygreen phenotype is a useful trait for productivity enhancement in hot-irrigated environments.

Source: Modelling and genetic dissection of staygreen under heat stress | SpringerLink

Resistance of Bt-maize (MON810) against the stem borers Busseola fusca (Fuller) and Chilo partellus (Swinhoe) and its yield performance in Kenya

Posted by gabrielamartinez on , in Journal Articles

A study was conducted to assess the performance of maize hybrids with Bt event MON810 (Bt-hybrids) against the maize stem borer Busseola fusca (Fuller) in a biosafety greenhouse (BGH) and against the spotted stem borer Chilo partellus (Swinhoe) under confined field trials (CFT) in Kenya for three seasons during 2013e2014. The study comprised 14 non-commercialized hybrids (seven pairs of near-isogenic Bt and non-Bt hybrids) and four non-Bt commercial hybrids. Each plant was artificially infested twice with 10 first instar larvae. In CFT, plants were infested with C. partellus 14 and 24 days after planting; in BGH, plants were infested with B. fusca 21 and 31 days after planting. In CFT, the seven Bt hybrids significantly differed from their non-Bt counterparts for leaf damage, number of exit holes, percent tunnel length, and grain yield. When averaged over three seasons, Bt-hybrids gave the highest grain yield (9.7 t ha1), followed by non-Bt hybrids (6.9 t ha1) and commercial checks (6 t ha1). Bt-hybrids had the least number of exit holes and percent tunnel length in all the seasons as compared to the non-Bt hybrids and commercial checks. In BGH trials, Bt-hybrids consistently suffered less leaf damage than their non-Bt near isolines. The study demonstrated that MON810 was effective in controlling B. fusca and
C. partellus. Bt-maize, therefore, has great potential to reduce the risk of maize grain losses in Africa due to stem borers, and will enable the smallholder farmers to produce high-quality grain with increased
yield, reduced insecticide inputs, and improved food security.

Source: Resistance of Bt-maize (MON810) against the stem borers Busseola fusca (Fuller) and Chilo partellus (Swinhoe) and its yield performance in Kenya

Variation in developmental patterns among elite wheat lines and relationships with yield, yield components and spike fertility

Posted by gabrielamartinez on , in Journal Articles

Developmental patterns strongly influence spike fertility and grain number, which are primarily deter-mined during the stem elongation period (i.e. time between terminal spikelet phase and anthesis). It has been proposed that the length of the stem elongation phase may, to an extent, affect grain number;thus it would be beneficial to identify genetic variation for the duration of this phase in elite germplasm. Variation in these developmental patterns was studied using 27 elite wheat lines in four experiments across three growing seasons. The results showed that the length of the stem elongation phase was (i)only slightly related to the period from seedling emergence to terminal spikelet, and (ii) more relevant than it for determining time to an thesis. Thus, phenological phases were largely independent and any particular time to an thesis may be reached with different combinations of component phases. Yield components were largely explained by fruiting efficiency of the elite lines used: the relationships were strongly positive and strongly negative with grain number and with grain weight, respectively. Although fruiting efficiency showed a positive trend with the duration of stem elongation that was not significant,a boundary function (which was highly significant) suggests that the length of this phase may impose an upper threshold for fruiting efficiency and grain number, and that maximum values of fruiting efficiency may require a relatively long stem elongation phase.

Source: Variation in developmental patterns among elite wheat lines and relationships with yield, yield components and spike fertility

Predicting wheat maturity and stay–green parameters by modeling spectral reflectance measurements and their contribution to grain yield under rainfed conditions

Posted by gabrielamartinez on , in Journal Articles

The normalized difference vegetation index (NDVI) continues to provide easy and fast methodologies to characterize wheat genetic resources in response to abiotic stresses. This study identifies ways to maximize green leaf area duration during grain filling and develops NDVI models to predict physiological maturity and different stay −green parameters to increase grain yield of rainfed winter wheat under terminal drought. Three wheat populations were evaluated: one containing 240 landraces from Afghanistan, the second with 250 modern lines and varieties, tested for two years under low rainfall conditions in Turkey, and the third with 291 landraces from Central and Western Asia (grown for one year in the same location). The onset of senescence, maximum “greenness”, rate of senescence and residual “greenness” at physiological maturity were estimated using sequential measurements of NDVI and have shown significant correlations with grain yield under low rainfall rainfed conditions. Trade-offs were identified among the different stay −green attributes, e.g. delayed onset of senescence and high maximum “greenness” resulted in accelerated rates of senescence and highest yields and were most evident in the landrace populations. It is concluded, that the use of rate of senescence to select for stay −green must be coupled with other stay −green components, e.g. onset of senescence or maximum “greenness” to avoid the effects of the trade-offs on final grain yield. The NDVI decay curves (using the last three NDVI measurements up to maturity) were used to estimate days to maturity using the NDVI decay during the senescence period and days to heading. A training and testing set (20 and 80% of each population, respectively) were used for calibrations allowing for correlations between predicted and observed maturity of up to r = +0.85 (P < 0.0001). This procedure will facilitate large −scale wheat phenotyping in the future.

Source: Predicting wheat maturity and stay–green parameters by modeling spectral reflectance measurements and their contribution to grain yield under rainfed conditions