Germplasm and Cultivar Development

Cool-season forage grasses have evolved, and continue to evolve, in natural ecosystems subject to environmental factors both in the presence and absence of human influences. The literature often lacks facts describing the evolution and domestication of forage grasses. Furthermore, the literature on this subject mainly deals with evolution of species in the broad scope, i.e., on a scale of hundreds of thousands or millions or years. Thus, some of our conclusions are necessarily speculative and are highly subject to the nature of the research that has been reported. We describe the forces of selection that act upon cool-season forage grasses and attempt to place each in historical perspective and in relation to each other. Because most economically important cool-season forage grasses are perennial, our principal focus will be on perennial species. There has been very little effort to quantify economic values of selection criteria or to empirically compare different breeding procedures in cool-season forage grasses. We attempt to summarize and compare some of the more important and thoroughly reported approaches used since the advent of formal breeding strategies in the late nineteenth and early twentieth centuries. These selection criteria and breeding procedures are as varied as the individual researchers who developed them. Examples are cited to illustrate principles and phenomena of historical or practical importance. More details of the agriculturally important species are discussed in the later chapters of this book. Space limitations prevent us from developing a thorough review, but we cite earlier reviews that thoroughly cover the first few decades of formal cool-season forage grass breeding. We also have summarized the limited amount of research on cool-season forage grasses where attempts have been made to use new technologies for hybridization, tissue culture, and genetic markers. Many of these techniques were first developed using other species and later adapted to cool-season forage grasses. Many are still undergoing rapid development and modification to allow more efficient use in breeding programs. Together they have had little practical impact on cool-season forage grass cultivars, but appear to offer considerable promise for creating new genetic variability and more efficient breeding procedures

Germplasm and Cultivar Development

Cool-season forage grasses have evolved, and continue to evolve, in natural ecosystems subject to environmental factors both in the presence and absence of human influences. The literature often lacks facts describing the evolution and domestication of forage grasses. Furthermore, the literature on this subject mainly deals with evolution of species in the broad scope, i.e., on a scale of hundreds of thousands or millions or years. Thus, some of our conclusions are necessarily speculative and are highly subject to the nature of the research that has been reported. We describe the forces of selection that act upon cool-season forage grasses and attempt to place each in historical perspective and in relation to each other. Because most economically important cool-season forage grasses are perennial, our principal focus will be on perennial species. There has been very little effort to quantify economic values of selection criteria or to empirically compare different breeding procedures in cool-season forage grasses. We attempt to summarize and compare some of the more important and thoroughly reported approaches used since the advent of formal breeding strategies in the late nineteenth and early twentieth centuries. These selection criteria and breeding procedures are as varied as the individual researchers who developed them. Examples are cited to illustrate principles and phenomena of historical or practical importance. More details of the agriculturally important species are discussed in the later chapters of this book. Space limitations prevent us from developing a thorough review, but we cite earlier reviews that thoroughly cover the first few decades of formal cool-season forage grass breeding. We also have summarized the limited amount of research on cool-season forage grasses where attempts have been made to use new technologies for hybridization, tissue culture, and genetic markers. Many of these techniques were first developed using other species and later adapted to cool-season forage grasses. Many are still undergoing rapid development and modification to allow more efficient use in breeding programs. Together they have had little practical impact on cool-season forage grass cultivars, but appear to offer considerable promise for creating new genetic variability and more efficient breeding procedures

Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites

Peer reviewedPublisher PD

Open access resources for genome-wide association mapping in rice.

Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement.Article number:10532

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive regions of the genome, long-read sequencing technologies are often used to perform phased de novo assembly. As a step toward reducing the cost and complexity of this type of analysis, we describe new methods for accurately phasing Oxford Nanopore Technologies (ONT) sequence data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse. We test using new variants of ONT PromethION sequencing, including those using proximity ligation, and show that newer, higher accuracy ONT reads substantially improve assembly quality

Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome

The domestication of Asian rice (Oryza sativa) was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers.In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV) consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations.Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species