Plant breeding can be broadly defined as alterations caused in plants as a result of their use by humans, ranging from unintentional changes resulting from the advent of agriculture to the application of molecular tools for precision breeding. The vast diversity of breeding methods can be simplified into three categories: (i) plant breeding based on observed variation by selection of plants based on natural variants appearing in nature or within traditional varieties; (ii) plant breeding based on controlled mating by selection of plants presenting recombination of desirable genes from different parents; and (iii) plant breeding based on monitored recombination by selection of specific genes or marker profiles, using molecular tools for tracking within-genome variation. The continuous application of traditional breeding methods in a given species could lead to the narrowing of the gene pool from which cultivars are drawn, rendering crops vulnerable to biotic and abiotic stresses and hampering future progress. Several methods have been devised for introducing exotic variation into elite germplasm without undesirable effects. Cases in rice are given to illustrate the potential and limitations of different breeding approaches.
Via Jean-Pierre Zryd
Neglected and underutilized species (NUS) are those to which little attention is paid or which are entirely ignored by agricultural researchers, plant breeders and policymakers1. Typically, NUS are not traded as commodities. They are wild or semi-domesticated varieties and non-timber forest species adapted to particular, often quite local, environments. Many of these varieties and species, along with a wealth of traditional knowledge about their cultivation and use, are being lost at an alarming rate. Yet NUS present tremendous opportunities for fighting poverty, hunger and malnutrition. And they can help make agricultural production systems more resilient to climate change. Not least, acknowledgment of the value of NUS in traditional foods and cultures can empower indigenous communities (women in particular) and reaffirm their identity. The time for action on NUS is now. There is a growing realization that agriculture must diversify. NUS have an important role to play in advancing agricultural development beyond the Green Revolution model of improving and raising the yields of staple crops.
Expression profiling is one of the most important tools for dissecting biological functions of genes and the upregulation or downregulation of gene expression is sufficient for recreating phenotypic differences. Expression divergence of genes significantly contributes to phenotypic variations. However, little is known on the molecular basis of expression divergence and evolution among rice genotypes with contrasting phenotypes. In this study, we have implemented an integrative approach using bioinformatics and experimental analyses to provide insights into genomic variation, expression divergence, and evolution between salinity-sensitive rice variety Nipponbare and tolerant rice line Pokkali under normal and high salinity stress conditions. We have detected thousands of differentially expressed genes between these two genotypes and thousands of up- or downregulated genes under high salinity stress. Many genes were first detected with expression evidence using custom microarray analysis. Some gene families were preferentially regulated by high salinity stress and might play key roles in stress-responsive biological processes. Genomic variations in promoter regions resulted from single nucleotide polymorphisms, indels (1–10 bp of insertion/deletion), and structural variations significantly contributed to the expression divergence and regulation. Our data also showed that tandem and segmental duplication, CACTA and hATelements played roles in the evolution of gene expression divergence and regulation between these two contrasting genotypes under normal or high salinity stress conditions.
Plants naturally emit methanol as volatile organic compound. Methanol is toxic to insect pests; but the quantity produced by most of the plants is not enough to protect them against invading insect pests. In the present study, we demonstrated that the over-expression of pectin methylesterase, derived fromArabidopsis thaliana and Aspergillus niger, in transgenic tobacco plants enhances methanol production and resistance to polyphagous insect pests. Methanol content in the leaves of transgenic plants was measured using proton nuclear spectroscopy (1H NMR) and spectra showed up to 16 fold higher methanol as compared to control wild type (WT) plants. A maximum of 100 and 85% mortality in chewing insectsHelicoverpa armigera and Spodoptera litura larvae was observed, respectively when fed on transgenic plants leaves. The surviving larvae showed less feeding, severe growth retardation and could not develop into pupae. In-planta bioassay on transgenic lines showed up to 99 and 75% reduction in the population multiplication of plant sap sucking pests Myzus persicae (aphid) and Bemisia tabaci (whitefly), respectively. Most of the phenotypic characters of transgenic plants were similar to WT plants. Confocal microscopy showed no deformities in cellular integrity, structure and density of stomata and trichomes of transgenic plants compared to WT. Pollen germination and tube formation was also not affected in transgenic plants. Cell wall enzyme transcript levels were comparable with WT. This study demonstrated for the first time that methanol emission can be utilized for imparting broad range insect resistance in plants.
My time with the Plant Breeding and Genomics Community of Practice on eXtension.org has been a fantastic opportunity to see plant breeding from a multi-crop and multi-trait perspective. It has been a privilege to be involved in plant breeding extension through the development of open-source tutorials (http://www.extension.org/plant_breeding_genomics) and Plant Breeding and Genomics News (http://www.scoop.it/t/plant-breeding-and-genomics-news). I look forward to applying this experience in my new position as Genotyping Support Scientist with the Generation Challenge Program. Thank you to everyone who contributes to the Plant Breeding Community of Practice.
Program The course covers the basics of DNA markers, quantitative trait loci and the transition from maker assisted selection with a highlight on breeding for disease resistance.
New for 2014! Extended modules on genomic selection, the latest integration of genomics to breeding, and a hands-on workshop on software support to marker application in breeding including the Integrated Breeding Platform and BLUPS.
Who should attend? The course is aimed at professionals who are directly or indirectly involved in plant breeding and germplasm improvement. It is an opportunity for breeders who are already using these tools to expand their knowledge of new strategies and technologies and for laboratory personnel to appreciate how the marker data that they generate are applied in breeding programs.
Field and greenhouse studies examined the effects of growth habit and chloroplast presence in leaf veins for their role in increasing agronomic water use efficiency and yields of California modern processing tomato (Solanum lycopersicum L.) cultivars. Five introgression lines (ILs), made with Solanum pennellii Cor. in the genetic background of cultivar M82, differ in genes that map to a region on Chromosome 5, including the SP5G gene (determinate vs. semideterminate (Det vs. SemiDet)) and the obv gene (presence (obscure) vs. absence (clear) of leaf vein chloroplasts (Obs vs. Clr)). The five ILs and M82 represented three of the four gene combinations (Det–Clr was unavailable). Det–Obs ILs had less leaf, stem and total aboveground biomass with earlier fruit set and ripening than SemiDet–Clr ILs. By harvest, total fruit biomass was not different among ILs. Photosynthetic rates and stomatal conductance were 4–7% and 13–26% higher, respectively, in Det–Obs ILs than SemiDet–Clr ILs. SemiDet–Obs ILs were intermediate for growth and gas exchange variables. The Det–Obs ILs had lower leaf N concentration and similar chlorophyll content per leaf area (but slightly higher per leaf mass) than SemiDet–Clr ILs. The Obs trait was associated with gains in leaf gas exchange-related traits. This study suggests that a more compact growth habit, less leaf biomass and higher C assimilation capacity per leaf area were relevant traits for the increased yields in cultivars with determinate growth. Developing new introgression libraries would contribute to understanding the multiple trait effects of desirable phenotypes.
Maize rough dwarf disease (MRDD) is a devastating viral disease that results in considerable yield losses worldwide. Three major strains of virus cause MRDD, including maize rough dwarf virus in Europe, Mal de Rio Cuarto virus in South America, and rice black-streaked dwarf virus in East Asia. These viral pathogens belong to the genus fijivirus in the family Reoviridae. Resistance against MRDD is a complex trait that involves a number of quantitative trait loci (QTL). The primary approach used to minimize yield losses from these viruses is to breed and deploy resistant maize hybrids.
Of the 50 heterogeneous inbred families (HIFs), 24 showed consistent responses to MRDD across different years and locations, in which 9 were resistant and 15 were susceptible. We performed trait-marker association analysis on the 24 HIFs and found six chromosomal regions which were putatively associated with MRDD resistance. We then conducted QTL analysis and detected a major resistance QTL, qMrdd1, on chromosome 8. By applying recombinant-derived progeny testing to self-pollinated backcrossed families, we fine-mapped the qMrdd1 locus into a 1.2-Mb region flanked by markers M103-4 and M105-3. The qMrdd1 locus acted in a recessive manner to reduce the disease-severity index (DSI) by 24.2--39.3%. The genetic effect of qMrdd1 was validated using another F6 recombinant inbred line (RIL) population in which MRDD resistance was segregating and two genotypes at the qMrdd1 locus differed significantly in DSI values.
The qMrdd1 locus is a major resistance QTL, acting in a recessive manner to increase maize resistance to MRDD. We mapped qMrdd1 to a 1.2-Mb region, which will enable the introgression of qMrdd1-based resistance into elite maize hybrids and reduce MRDD-related crop losses.
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
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Most methods for next-generation sequencing (NGS) data analyses incorporate information regarding allele frequencies using the assumption of Hardy–Weinberg equilibrium (HWE) as a prior. However, many organisms including those that are domesticated, partially selfing, or with asexual life cycles show strong deviations from HWE. For such species, and specially for low-coverage data, it is necessary to obtain estimates of inbreeding coefficients (F) for each individual before calling genotypes. Here, we present two methods for estimating inbreeding coefficients from NGS data based on an expectation-maximization (EM) algorithm. We assess the impact of taking inbreeding into account when calling genotypes or estimating the site frequency spectrum (SFS), and demonstrate a marked increase in accuracy on low-coverage highly inbred samples. We demonstrate the applicability and efficacy of these methods in both simulated and real data sets.
Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r2>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates.
On Wednesday, Nov. 6, 2013, two speakers will describe the latest efforts to identify and protect the wild relatives of domesticated crop plants around the globe. The presentations are part of the American Society of Agronomy (ASA), Crop Science Society of America (CSSA), and Soil Science Society of America (SSSA) International Annual Meetings, Nov. 3-6 in Tampa, Florida.
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Members of the American Society of Agronomy, Crop Science Society of America, and the Soil Science Society of American can livestream many of the upcoming talks. Register to livestream
Physiological and developmental traits that vary over time are difficult to phenotype under relevant growing conditions. In this light, we developed a novel system for phenotyping dynamic traits in the field. System performance was evaluated on 25 Pima cotton (Gossypium barbadense L.) cultivars grown in 2011 at Maricopa, Arizona. Field-grown plants were irrigated under well watered and water-limited conditions, with measurements taken at different times on 3 days in July and August. The system carried four sets of sensors to measure canopy height, reflectance and temperature simultaneously on four adjacent rows, enabling the collection of phenotypic data at a rate of 0.84 ha h–1. Measurements of canopy height, normalised difference vegetation index and temperature all showed large differences among cultivars and expected interactions of cultivars with water regime and time of day. Broad-sense heritabilities (H2)were highest for canopy height (H2 = 0.86–0.96), followed by the more environmentally sensitive normalised difference vegetation index (H2 = 0.28–0.90) and temperature (H2 = 0.01–0.90) traits. We also found a strong agreement (r2 = 0.35–0.82) between values obtained by the system, and values from aerial imagery and manual phenotyping approaches. Taken together, these results confirmed the ability of the phenotyping system to measure multiple traits rapidly and accurately.