The narrow genetic base of cultivars coupled with low utilization of genetic resources are the major factors limiting grain legume production and productivity globally. Exploitation of new and diverse sources of variation is needed for the genetic enhancement of grain legumes. Wild relatives with enhanced levels of resistance/tolerance to multiple stresses provide important sources of genetic diversity for crop improvement. However, their exploitation for cultivar improvement is limited by cross-incompatibility barriers and linkage drags. Pre-breeding provides a unique opportunity, through the introgression of desirable genes from wild germplasm into genetic backgrounds readily used by the breeders with minimum linkage drag, to overcome this. Pre-breeding activities using promising landraces, wild relatives, and popular cultivars have been initiated at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) to develop new gene pools in chickpea, pigeonpea, and groundnut with a high frequency of useful genes, wider adaptability, and a broad genetic base. The availability of molecular markers will greatly assist in reducing linkage drags and increasing the efficiency of introgression in pre-breeding programs.

We estimate the minimum core size necessary to maximally represent a portion of the U.S. Department of Agriculture's National Plant Germplasm System apple (Malus) collection. We have identified a subset of Malus sieversii individuals that complements the previously published core subsets for two collection sites within Kazakhstan. We compared the size and composition of this complementary subse...

Simple sequence repeats (SSRs) were used to assess genetic diversity and study genetic relatedness in a large collection of Malus germplasm. A total of 164 accessions from the Malus core collection, maintained at the University of Illinois, were genotyped using apple SSR markers. Each of the accessions was genotyped using a single robust SSR marker from each of the 17 different linkage groups in Malus . Data were subjected to principal component analysis, and a dendrogram was constructed to establish genetic relatedness. As expected, this diverse core collection showed high allelic diversity; moreover, this allelic diversity was higher than that previously reported. Cluster analysis revealed the presence of four distinct clusters of accessions in this collection.

Abstract released cultivars, breeding and genetics programs have also focused attention on other resistance sources in The Russian wheat aphid (Diuraphis noxia (Mordvilko), RWA) efforts to broaden the resistance base. These efforts were used as susceptible checks while the germplasm line 94M370 (Dn7 resistance gene) was used as a resistant check. Evaluation of Porter, USDA-ARS, 2004, personal communication) has accessions showing at least a moderate level of resistance in unrepli- spread to other areas of Colorado (unpublished data, cated tests was repeated with three replications in a randomized com- 2004) and has been identified in collections from neigh- plete block design. Forty-four germplasm accessions were identified boringstates(e.g.,KansasandNebraska;J.Burd,USDA- as having high to moderate levels of resistance to Biotype 2 RWA. ARS, 2004, personal communication). The identifica- Most of these accessions originated from areas of the world where tion and rapid spread of this new biotype is of great RWA is endemic or were derived from germplasm accessions that concern because no Biotype 2 resistant cultivars or ger- originated from these areas. Ten accessions showed a level of resis- mplasm sources are currently available for resistance tance comparable with the 94M370 check. These accessions should breeding (Haley et al., 2004a), with the exception of the prove useful in future genetic studies and for breeding for resistance 94M370 germplasm accession that carries the Dn7 gene.

Marker-assisted selection (MAS) is often employed in crop breeding programs to accelerate and enhance cultivar development, via selection during the juvenile phase and parental selection prior to crossing. Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery. To bridge the gap between marker development and MAS implementation, this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery, low-cost genotyping through amplicon sequencing (AmpSeq) and decision making. The results document the development of a MAS package derived from genotyping-by-sequencing using three traits (flower sex, disease resistance and acylated anthocyanins) in grapevine breeding. The vast majority of sequence reads (8299%) were from the targeted regions. Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data, most amplicons (83 to 87%) had <10% missing data, and read depth had a median of 220–244×. Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy, flexibility, speed, high-throughput, low-cost and easily automated analysis.

Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world. The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits. The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.

The United States Department of Agriculture, Soybean Germplasm Collection includes 18,480 domesticated soybean and 1168 wild soybean accessions introduced from 84 countries or developed in the United States. This collection was genotyped with the SoySNP50K BeadChip containing greater than 50K single-nucleotide polymorphisms. Redundant accessions were identified in the collection, and distinct genetic backgrounds of soybean from different geographic origins were observed that could be a unique resource for soybean genetic improvement. We detected a dramatic reduction of genetic diversity based on linkage disequilibrium and haplotype structure analyses of the wild, landrace, and North American cultivar populations and identified candidate regions associated with domestication and selection imposed by North American breeding. We constructed the first soybean haplotype block maps in the wild, landrace, and North American cultivar populations and observed that most recombination events occurred in the regions between haplotype blocks. These haplotype maps are crucial for association mapping aimed at the identification of genes controlling traits of economic importance. A case-control association test delimited potential genomic regions along seven chromosomes that most likely contain genes controlling seed weight in domesticated soybean. The resulting dataset will facilitate germplasm utilization, identification of genes controlling important traits, and will accelerate the creation of soybean varieties with improved seed yield and quality.

Incorporation of genetic diversity into elite wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) cultivars has long been recognized as ameans of improving wheat productivity and securing global wheat supply. Synthetic hexaploid wheat (SHW) genotypes recreated from its two progenitor species, the tetraploid, Triticum turgidum (2n = 4x = 28, AABB) and its diploid wild relative, Aegilops tauschii (2n = 2x = 14, DD) are a useful resource of newgenes for hexaploidwheat improvement. These include many productivity traits such as abiotic (drought, heat, salinity/sodicity, and waterlogging) and biotic (rusts, septoria, barley yellow dwarf virus (BYDV), crownrot, tanspot, spot blotch, nematodes,powderymildew, and fusarium head blight) stress resistance/tolerances as well as novel grain quality traits. Numerous SHWs have been produced globally by various institutions including CIMMYT-Mexico, ICARDA-Syria, Department of Primary Industries (DPI), Victoria-Australia, IPK-Germany, Kyoto University-Japan, and USDAARS. This review examines the varied aspects in the utilization of synthetics for wheat improvement including the traits and genes identified, mapped, and transferred to common wheat. It has also been demonstrated that synthetic backcross-derived lines (SBLs, i.e., when SHW is crossed to adapted local bread varieties) show significant yield increases and thus, enhanced yield performance across a diverse range of environments, demonstrating their potential for improving wheat productivity worldwide. This is particularly evident in moisturelimited environments. The use of SBLs, advanced backcross QTL analysis, chromosome introgression lines, and whole genome association mapping is contributing to the elucidation of the genetic architecture of some of the traits. The contribution of transgressive segregation to enhanced phenotypes and the mechanisms including its genetic and physiological basis are yet to be elucidated. Understanding these would further enhance the utility of SBLs. Considerable progress has beenmade in the identification of useful quantitative trait loci (QTL) and genes, however the transfer of such rich genetic diversity into elite wheat cultivars is still quite limited. Gaps still exist in data cataloging; and access to such information could serve as an important community resource. Future production of new SHWshould extend to under-exploited AB genome tetraploids such as T. turgidum ssp. carthlicum, T. turgidum ssp. dicoccum, and T. turgidum ssp. dicoccoides and identifying gaps in the Ae. tauschii germplasm used for existing SHW. Identifying geographical areas where the progenitor species of the existing SHWwere collectedwould assist in guiding future collectionmissions.The recent advances in molecular technologies with whole genome sequencing becoming affordable will provide researchers with opportunities for more detailed analysis of traits and the deployment of more efficient strategies in the use of the unique exotic alleles derived from SHW for common wheat improvement. Thus, the contribution of SHWand the derived SBLs to wheat cropping systems worldwide is likely to grow in significance. However, these potential benefits are only realizable if phenotyping is equally extensive and effective. 漏 2013 Wiley-Blackwell. Published 2013 by John Wiley and Sons, Inc.

Two main questions in programs introgressing exotic maize germplasm into temperate materials are the choice of available exotic sources to work with, and the proportion of exotic germplasm that should be incorporated into adapted germplasm. The objectives of this study were to compare effects of the different proportions of tropical maize germplasm (via inbred NC298) in hybrids male parent, on... [Show full abstract]