Genomics-Assisted Crop Improvement

Abstract

Who would have believed only two decades ago that plant scientists would have access to nearly the complete genetic code of numerous plant species, including major crop species. The idea of having ready access to whole genome sequences encompassing 140 million bases of the model plant Arabidopsis seemed like science fiction, let alone having available even larger genomes such as rice at 430 Mb or maize at 2500 Mb (the same size as the human genome). And then proceeding to identify variation beyond what was anticipated, such as the 2.6 SNPs (Single Nucleotide Polymorphisms) per kb in rice. The number of strains of various species with literally hundreds of thousands of inserts, allowing the association of sequence and trait, increased at an unanticipated rate. Who would have believed only a decade ago that we would be capable of analyzing the expression of genes across the whole genome and matching that profile with traits of interest. And now the area of metabolomics is allowing even more meaningful explanations of the genetic control of important traits.This book brings all of these advances in genomics to the forefront and prepares the plant scientists for the next decade. Important technologies are discussed such as association mapping, simulation modeling, and development of appropriate populations including the advanced backcross and introgression-lines for incorporating traits into useful genetic materials. Such approaches are facilitating the identification of traits that are not obvious simply from observing the plant phenotype, and they provide ways to extract new and useful traits from wild related species. Comparing the genomic information across broadly-related species has generated important evolutionary information. In addition, the common occurrence of duplicated segments and large gene families with partially redundant or tissue-and developmentally-specific expression will lead to information fundamental to plant performance.Methods for the identification of genes underlying traits are improving every day. The association of allelic variation in a candidate gene and a trait is leading to much greater understanding of the genetic control of traits. Numerous transcription factors and even non-coding sequences are being implicated as the basis of considerable genetic variation. Forward and reverse genetics are both found to be very useful in revealing gene-trait associations.The tremendous expansion of genomic analytical approaches along with efforts to reduce the cost, together with appropriate statistical designs and analyses, are xi xii FOREWORD making it easier and more expeditious to use the ever-increasing sequence information to identify useful genes. This body of knowledge in plant genomics and its myriad of applications are nicely reflected in this book.