Greenhouse Gas Emissions and Management Practices that Affect Emissions in US Rice Systems.

Previous reviews have quantified factors affecting greenhouse gas (GHG) emissions from Asian rice ( L.) systems, but not from rice systems typical for the United States, which often vary considerably particularly in practices (i.e., water and carbon management) that affect emissions. Using meta-analytic and regression approaches, existing data from the United States were examined to quantify GHG emissions and major practices affecting emissions. Due to different production practices, major rice production regions were defined as the mid-South (Arkansas, Texas, Louisiana, Mississippi, and Missouri) and California, with emissions being evaluated separately. Average growing season CH emissions for the mid-South and California were 194 (95% confidence interval [CI] = 129-260) and 218 kg CH ha season (95% CI = 153-284), respectively. Growing season NO emissions were similar between regions (0.14 kg NO ha season). Ratoon cropping (allowing an additional harvestable crop to grow from stubble after the initial harvest), common along the Gulf Coast of the mid-South, had average CH emissions of 540 kg CH ha season (95% CI = 465-614). Water and residue management practices such as alternate wetting and drying, and stand establishment method (water vs. dry seeding), and the amount of residue from the previous crop had the largest effect on growing season CH emissions. However, soil texture, sulfate additions, and cultivar selection also affected growing season CH emissions. This analysis can be used for the development of tools to estimate and mitigate GHG emissions from US rice systems and other similarly mechanized systems in temperate regions.

Genetic Mapping of Quantitative Trait Loci for Grain Yield under Drought in Rice under Controlled Greenhouse Conditions.

Drought stress is a constant threat to rice production worldwide. Most modern rice cultivars are sensitive to drought, and the effect is severe at the reproductive stage. Conventional breeding for drought resistant (DR) rice varieties is slow and limited due to the quantitative nature of the DR traits. Identification of genes (QTLs)/markers associated with DR traits is a prerequisite for marker-assisted breeding. Grain yield is the most important trait and to this end drought yield QTLs have been identified under field conditions. The present study reports identification of drought yield QTLs under controlled conditions without confounding effects of other factors prevalent under natural conditions. A linkage map covering 1,781.5 cM with an average resolution of 9.76 cM was constructed using an F2 population from a cross between two Japonica cultivars, Cocodrie (drought sensitive) and Vandana (drought tolerant) with 213 markers distributed over 12 rice chromosomes. A subset of 59 markers (22 genic SSRs and 37 SNPs) derived from the transcriptome of the parents were also placed in the map. Single marker analysis using 187 F2 : 3 progeny identified 6 markers distributed on chromosomes 1, 5, and 8 to be associated with grain yield under drought (GYD). Composite interval mapping identified six genomic regions/quantitative trait loci (QTL) on chromosome 1, 5, 8, and 9 to be associated with GYD. QTLs located on chromosome 1 (qGYD1.2, qGYD1.3), chromosome 5 (qGYD5.1) and chromosome 8 (qGYD8.1) were contributed by Vandana alleles, whereas the QTLs, qGYD1.1 and qQYD9.1 were contributed by Cocodrie alelles. The additive positive phenotypic variance explained by the QTLs ranged from 30.0 to 34.0%. Candidate genes annotation within QTLs suggested the role of transcription factors and genes involved in osmotic potential regulation through catalytic/metabolic pathways in drought tolerance mechanism contributing to yield.

Mutational breeding and genetic engineering in the development of high grain protein content.

Cereals are the most important crops in the world for both human consumption and animal feed. Improving their nutritional values, such as high protein content, will have significant implications, from establishing healthy lifestyles to helping remediate malnutrition problems worldwide. Besides providing a source of carbohydrate, grain is also a natural source of dietary fiber, vitamins, minerals, specific oils, and other disease-fighting phytocompounds. Even though cereal grains contain relatively little protein compared to legume seeds, they provide protein for the nutrition of humans and livestock that is about 3 times that of legumes. Most cereal seeds lack a few essential amino acids; therefore, they have imbalanced amino acid profiles. Lysine (Lys), threonine (Thr), methionine (Met), and tryptophan (Trp) are among the most critical and are a limiting factor in many grain crops for human nutrition. Tremendous research has been put into the efforts to improve these essential amino acids. Development of high protein content can be outlined in four different approaches through manipulating seed protein bodies, modulating certain biosynthetic pathways to overproduce essential and limiting amino acids, increasing nitrogen relocation to the grain through the introduction of transgenes, and exploiting new genetic variance. Various technologies have been employed to improve protein content including conventional and mutational breeding, genetic engineering, marker-assisted selection, and genomic analysis. Each approach involves a combination of these technologies. Advancements in nutrigenomics and nutrigenetics continue to improve public knowledge at a rapid pace on the importance of specific aspects of food nutrition for optimum fitness and health. An understanding of the molecular basis for human health and genetic predisposition to certain diseases through human genomes enables individuals to personalize their nutritional requirements. It is critically important, therefore, to improve grain protein quality. Highly nutritious grain can be tailored to functional foods to meet the needs for both specific individuals and human populations as a whole.

Current patents and future development underlying marker-assisted breeding in major grain crops.

Genomics and molecular markers provide new tools to assemble and mobilize important traits from different genetic backgrounds, including breeding lines and cultivars from different parts of the world and their related wild ancestors, to improve the quality and yield of the existing commercial cultivars to meet the increasing challenges of global food demand. The basic techniques of marker-assisted breeding, such as isolating DNA, amplifying DNA of interest using publicly available primers, and visualizing DNA fragments using standard polyacrylamid gel, have been described in the literature and, therefore, are available to scientists and breeders without any restrictions. A more sophisticated high-throughput system that includes proprietary chemicals and reagents, parts and equipments, software, and methods or processes, has been a subject of intensive patents and trade secrets. The high-throughput systems offer a more efficient way to discover associated QTLs for traits of economic importance. Therefore, an increasing number of patents of highly valued genes and QTLs is expected. This paper will discuss and review current patents associated with genes and QTLs utilized in marker-assisted breeding in major grain crops. The availability of molecular markers for important agronomic traits combined with more efficient marker detection systems will help reach the full benefit of MAS in the breeding effort to reassemble potential genes and recapture critical genes among the breeding lines that were lost during domestication to help boost crop production worldwide.