Posts Tagged ‘Plant Breeding’

A direct comparison of remote sensing approaches for high-throughput phenotyping in plant breeding

Posted by gabrielamartinez on , in Journal Articles

57986Authors: Tattaris, M., Reynolds, M.P., Chapman, S.

Published in:  Frontiers in Plant Science, 2016, vol.7, no.1131

Remote sensing (RS) of plant canopies permits non-intrusive, high-throughput monitoring of plant physiological characteristics. This study compared three RS approaches using a low flying UAV (unmanned aerial vehicle), with that of proximal sensing, and satellite-based imagery. Two physiological traits were considered, canopy temperature (CT) and a vegetation index (NDVI), to determine the most viable approaches for large scale crop genetic improvement. The UAV-based platform achieves plot-level resolution while measuring several hundred plots in one mission via high-resolution thermal and multispectral imagery measured at altitudes of 30–100 m. The satellite measures multispectral imagery from an altitude of 770 km. Information was compared with proximal measurements using IR thermometers and an NDVI sensor at a distance of 0.5–1 m above plots. For robust comparisons, CT and NDVI were assessed on panels of elite cultivars under irrigated and drought conditions, in different thermal regimes, and on un-adapted genetic resources under water deficit. Correlations between airborne data and yield/biomass at maturity were generally higher than equivalent proximal correlations. NDVI was derived from high-resolution satellite imagery for only larger sized plots (8.5 × 2.4 m) due to restricted pixel density. Results support use of UAV-based RS techniques for high-throughput phenotyping for both precision and efficiency.


Molecular Breeding for Quality Protein Maize (QPM)

Posted by Carelia Juarez on , in Journal Articles

Molecular Breeding for Quality Protein Maize (QPM). 2014. Babu, R.; Prasanna, B.M. p. 489-505. In: Genomics of Plant Genetic Resources; Vol. 2 Crop productivity, food security and nutritional quality. Tuberosa, R.; Graner, A.; Frison, E. (Eds.). Netherlands:  Springer.

98827Maize endosperm protein is deficient in two essential amino acids, lysine and tryptophan. Several spontaneous and induced mutations that affect amino acid composition in maize have been discovered amongst which the o2 gene (opaque2) has been used in association with endosperm and amino acid modifier genes for developing Quality Protein Maize (QPM), which contains almost double the amount of endosperm lysine and tryptophan as compared to the normal/non-QPM maize. These increases have been shown to have dramatic impacts on human and animal nutrition, growth and performance. A range of hard endosperm QPM germplasm has been developed at the International Maize and Wheat Improvement Center (CIMMYT) mostly through conventional breeding approaches to meet the requirements of various maize growing regions across the world. Microsatellite markers located within the o2 gene provided opportunities for accelerating the pace of QPM conversion programs through marker-assisted selection (MAS). More recently, CIMMYT scientists are striving to develop reliable, easy-to-use markers for endosperm hardness and free amino acid content in the maize endosperm. Recent technological developments including high throughput, single seed-based DNA extraction, coupled with low-cost, high density SNP genotyping strategies, and breeder-ready markers for some key adaptive traits in maize, promise enhanced efficiency and cost effectiveness of MAS in QPM breeding programs. Here, we present a summary of QPM research and breeding with particular emphasis on genetic and molecular basis of o2, epistasis between o2 and other high-lysine mutant genes, and the recent advances in genomics technologies that could potentially enhance the efficiency of molecular breeding for QPM in the near future.

CIMMYT Annual Report 2013: Agricultural research for development to improve food and nutritional security

Posted by Carelia Juarez on , in CIMMYT Publications

CIMMYT Annual Report 2013: Agricultural research for development to improve food and nutritional security. 2014. CIMMYT, Int.. : 136 p.. Mexico, DF (Mexico). CIMMYT. Series: CIMMYT Annual Report

99444.pdfThrough research, development, training and capacity building, CIMMYT works with partners to sustainably increase the productivity of maize- and wheat-based cropping systems. Focused on improving food and nutritional security and improving livelihoods in the developing world, CIMMYT is a member of CGIAR and leads the MAIZE and WHEAT CGIAR Research Programs (CRPs)..


Maize hybrid seed production manual

Posted by Carelia Juarez on , in CIMMYT Publications

Maize hybrid seed production manual2014MacRobert, J.Setimela, P.S.Gethi, J.Regasa, M.W. Mexico, DF (Mexico)CIMMYT v, 26 p. 

98078Maize hybrid seed provides farmers with varieties  containing improved genetics, such as high yield  potential and unique trait combinations to counter  diseases and adverse growing conditions. However,  the quality of hybrid seed depends greatly on  field production methods, both in adherence to  quality assurance standards and implementation of appropriate agronomic management. While open pollinated maize seed production is relatively straightforward, hybrid seed production requires additional field practices that are critical to success.

Genome-wide association analysis for nine agronomic traits in maize under well-watered and water-stressed conditions

Posted by Carelia Juarez on , in Journal Articles

Published in Theoretical and Applied Genetics 126 (10) : 2587-2596, 2013

Yadong Xue; Warburton, M.L.; Sawkins, M.; Xuehai Zhang; Setter, T.; Yunbi Xu; Grudloyma, P.; Gethi, J.; Ribaut, J-M; Wanchen Li; Xiaobo Zhang; Yonglian Zheng; Jianbing Yan

Drought can cause severe reduction in maize production, and strongly threatens crop yields. To dissect this complex trait and identify superior alleles, 350 tropical and subtropical maize inbred lines were genotyped using a 1536-SNP array developed from drought-related genes and an array of 56,110 random SNPs. The inbred lines were crossed with a common tester, CML312, and the testcrosses were phenotyped for nine traits under well-watered and water-stressed conditions in seven environments. Using genome-wide association mapping with correction for population structure, 42 associated SNPs (P ≤ 2.25 × 10−6 0.1/N) were identified, located in 33 genes for 126 trait × environment × treatment combinations. Of these genes, three were co-localized to drought-related QTL regions. Gene GRMZM2G125777 was strongly associated with ear relative position, hundred kernel weight and timing of male and female flowering, and encodes NAC domain-containing protein 2, a transcription factor expressed in different tissues. These results provide some good information for understanding the genetic basis for drought tolerance and further studies on identified candidate genes should illuminate mechanisms of drought tolerance and provide tools for designing drought-tolerant maize cultivars tailored to different environmental scenarios.

CIMMYT Annual Report 2012: Agricultural research for development improves food security

Posted by Carelia Juarez on , in CIMMYT Publications

CIMMYT Annual Report 2012: Agricultural research for development improves food security. 2013. CIMMYT, Int.. : 28 p.. Mexico, DF (Mexico). CIMMYT. Series: CIMMYT Annual Report.

98208.pdfThe work of CIMMYT and its many valued partners on maize and wheat farming systems is more  important now than at any time in the organization’s history. Our planet’s expanding population,  changing diets, limited natural resources, demand for bio-fuels and increasingly variable climate  are all putting extraordinary pressure on the global food system. The evidence is all around us. In  2012, for the third time in less than six years, we faced a global food price crisis with international  maize prices reaching levels double those of just two years prior. In the wake of the Arab Spring,  two major wheat production and cereal importing areas, North Africa and the Middle East, remain  highly stressed by rising wheat prices. In recent years average wheat imports for all of Africa have  reached more than 35 million tons annually, costing the continent’s nations more than US$12 billion and threatening the supply of wheat products for resource-poor consumers.

Effectiveness of selection at CIMMYT’s main maize breeding sites in Mexico for performance at sites in Africa and vice versa

Posted by Carelia Juarez on , in Journal Articles

Published in Plant Breeding 132 (3) : 299-304, 2013

Aida Z. Kebede, George Mahuku, Juan Burgueño, Felix San Vicente, Jill E. Cairns, Biswanath Das, Dan Makumbi, Cosmos Magorokosho, Vanessa S. Windhausen, Albrecht E. Melchinger and Gary N. Atlin

 The exchange of elite breeding materials across regions is an important way in which multinational maize breeding programmes access new genetic variation, improve efficiency and reduce costs. Our objectives were to examine whether CIMMYT’s breeding programmes for tropical and subtropical environments in Mexico and Eastern and Southern Africa (ESA) can effectively share materials. Sets of selected and unselected lines were evaluated for per se and testcross performance in multiple environments in Mexico and ESA for grain yield, days to anthesis and plant height. Genotypic correlations between performance in Mexico and ESA as testcross and line per se were high (≥ 0.72) for all experiments, and indirect selection efficiency ranged from 67 to over 100% for all traits. Lines selected in ESA or Latin America performed equally well in each region, indicating selection was for broad rather than regional adaptation. Thus, breeding programmes of CIMMYT in both Mexico and ESA can benefit tremendously by exchanging breeding materials and test results, and elite selections from each region should be fast-tracked for evaluation in the other.

Root-lodging resistance in maize as an example for high-throughput genetic mapping via single nucleotide polymorphism-based selective genotyping

Posted by Carelia Juarez on , in Journal Articles

Published in Plant Breeding 132 (1) : 90-98, 2013

Mohammad Farkhari, Alan Krivanek, Yunbi Xu, Tingzhao Rong, Mohammad R. Naghavi, Bahman Y. Samadi and Yanli Lu

Large-scale selective genotyping and high-throughput analysis are two important strategies for low-cost and high-effective genetic mapping. In this study, selective genotyping was applied to four maize F2 populations. Thirty plants were selected from each of the two tails of the original F2 populations to represent extreme resistant and susceptible plants to root lodging, and genotyped individually with 1536 single nucleotide polymorphisms (SNPs). A quantitative trait locus (QTL) was declared when at least three closely linked SNPs showed significant allele frequency difference between the two tails. Nine QTL were identified for root lodging across the four populations, which were located on chromosomes 2, 4, 5, 7, 8 and 10 and one of them was shared between two populations. A total of 20 segregation distortion regions (SDRs) were identified across the four populations, one of which was co-localized with a QTL on chromosome 4. The tightly linked SNPs identified in this study can be used for marker-assisted selection for root lodging. Selective genotyping, when combined with pooled DNA analysis, can be used to develop strategies for high-throughput genetic mapping for all crops.


Multi-environment QTL analyses for drought-related traits in a recombinant inbred population of chickpea (Cicer arientinum L.)

Posted by Carelia Juarez on , in Journal Articles

Published in Theoretical and Applied Genetics, 2013

A. Hamwieh, M. Imtiaz and R. S. Malhotra

A recombinant inbred line (RIL) population, comprising 181 lines derived from ILC588 × ILC3279, was evaluated in 10 environments across three locations with different moisture gradients. A drought resistance score (DRS) and three phenology traits—plant height (PLHT), days to flowering (DFLR), and days to maturity (MAT)—were recorded along with seven yield-related traits—grain yield (GY), biological yield (BY), harvest index (HI), the number of pods/3 plants (Pod), percentage of empty pods (%Epod), 100 seed weight (100 sw), and seed number/3 plants (SN). Two RILs (152, 162) showed the best GYs and DRSs under stressed and non-stressed environments. The quantitative trait loci (QTLs) analyses detected 93 significant QTLs (LOD ≥ 2.0) across the genome × environment interactions. The highest phenotypic variation (>24 %) was explained by the QTLDFLR in Terbol-11. Four common possible pleiotropic QTLs on LG3 and LG4 were identified as associated with DFLR, DRS, GY, MAT, HI, SN, and Pod. No significant epistatic interactions were found between these QTLs and the other markers. However, the QTL for DRS was detected as a conserved QTL in three late planting environments. The markers H6C-07 (on LG3) and H5G01 (on LG4) were associated with QTLs for many traits in all environments studied except two. The allele ‘A’ of marker H6C07 (from the tolerant parent ILC588) explained 80 % of the yield increase under late planting and 29.8 % of that under dry environments. Concentrating on LG3 and LG4 in molecular breeding programs for drought could speed up improvement for these traits.


Accelerated development of quality protein maize hybrid through marker-assisted introgression of opaque-2 allele

Posted by Carelia Juarez on , in Journal Articles

Published in Plant Breeding, 2012

Hari S. Gupta, Babu Raman, Pawan K. Agrawal, Vinay Mahajan, Firoz Hossain and Nepolean Thirunavukkarasu

Vivek Maize Hybrid 9- a popular single-cross hybrid developed by crossing CM 212 and CM 145 was released for commercial cultivation in India. The parental lines, being deficient in lysine and tryptophan, were selected for introgression of opaque-2 allele using CML 180 and CML 170 as donor lines through marker-assisted backcross breeding. The opaque-2 homozygous recessive genotypes with >90% recovery of the recurrent parent genome were selected in BC2F2, and the seeds with <25% opaqueness in BC2F3 were forwarded for seed multiplication. Vivek Quality Protein Maize (QPM) 9, the improved QPM hybrid, showed 41% increase in tryptophan and 30% increase in lysine over the original hybrid. The grain yield of the improved hybrid was on par with the original hybrid. The newly improved QPM maize hybrid released in 2008 will help in reducing the protein malnutrition because its biological value is superior over the normal maize hybrids. This short duration QPM maize hybrid has been adopted in several hill states of North Western and North Eastern Himalayan regions.