Common bean (Phaseolus vulgaris L.), one of the most important grain legume crops for direct human consumption, faces many challenges as a crop. Domesticated from wild relatives that inhabit a relatively narrow ecological niche, common bean faces a wide range of biotic and abiotic constraints within its diverse agroecological settings. Biotic stresses impacting common bean include numerous bacterial, fungal, and viral diseases and various insect and nematode pests, and abiotic stresses include drought, heat, cold, and soil nutrient deficiencies or toxicities. Breeding is often local, focusing on improvements in responses to biotic and abiotic stresses that are particular challenges in certain locations and needing to respond to conditions such as day-length regimes. This review describes the major breeding objectives for common bean, followed by a description of major genetic and genomic resources, and an overview of current and prospective marker-assisted methods in common bean breeding. Improvements over traditional breeding methods in CB can result from the use of different approaches. Several important germplasm collections have been densely genotyped, and relatively inexpensive SNP genotyping platforms enable implementation of genomic selection and related markerassisted breeding approaches. Also important are sociological insights related to demand-led breeding, which considers local value chains, from farmers to traders to retailers and consumers.

Analysis of the sequences of 74 randomly selected BACs demonstrated that the maize nuclear genome contains Ϸ37,000 candidate genes with homologues in other plant species. An additional Ϸ5,500 predicted genes are severely truncated and probably pseudogenes. The distribution of genes is uneven, with Ϸ30% of BACs containing no genes. BAC gene density varies from 0 to 7.9 per 100 kb, whereas most gene islands contain only one gene. The average number of genes per gene island is 1.7. Only 72% of these genes show collinearity with the rice genome. Particular LTR retrotransposon families (e.g., Gyma) are enriched on gene-free BACs, most of which do not come from pericentromeres or other large heterochromatic regions. Gene-containing BACs are relatively enriched in different families of LTR retrotransposons (e.g., Ji). Two major bursts of LTR retrotransposon activity in the last 2 million years are responsible for the large size of the maize genome, but only the more recent of these is well represented in gene-containing BACs, suggesting that LTR retrotransposons are more efficiently removed in these domains. The results demonstrate that sample sequencing and careful annotation of a few randomly selected BACs can provide a robust description of a complex plant genome.gene distribution ͉ gene number ͉ genome annotation ͉ repetitive DNA ͉ sample sequencing W hole-genome sequence analysis has revolutionized the field of plant genetics. A sequenced plant genome provides the full list of genetic elements and also the context in which these elements function. The near-complete sequence of Arabidopsis thaliana (1) enabled the Arabidopsis 2010 project, which proposes to characterize the function of all of the genes in the genome (2). In addition, comparative analysis of the genomes of two or more species with known evolutionary relatedness is a powerful way to identify functional elements, to transfer knowledge from well studied model organisms to related plants, and to infer the mechanisms of genome evolution. For example, comparative analysis of orthologous regions from multiple cereals, including maize, rice, sorghum and wheat, has provided abundant information about the timing, nature and mechanisms of small rearrangements within those genomes (3-7).

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Therefore mapping mutants of CLGs 6 and 8 can enhance the identification of genes affecting important Mapping mutants of classical linkage groups 6 and 8 (CLGs 6 and agronomic traits. 8) in soybean [Glycine max (L.) Merr.] can enhance the identification of important agronomic traits. Genetic data suggest that CLGs 6 and Factors such as the type of genetic data, environment, 8 may belong to the same linkage group. Our objectives were to genetic background, genotype ϫ environment interacdetermine if CLGs 6 and 8 are the same or different linkage groups tion, and the linkage phase can influence recombination and to determine the gene order. Genotypes containing mutants of and result in a range of recombination values. The dif-CLGs 6 and 8 and mutants of other CLGs were crossed in various ferences between recombination values obtained from combinations. Data for the different characters were collected from backcross data, F 2 populations, and F 2:3 families have F 2 populations and F 2:3 families. Recombination values confirmed that been documented (Allard, 1956; Haldane, 1919; Immer, CLG 6 characters, Df 2 and Y 11 were linked (R ϭ 27.0 Ϯ 5.9), Df 2 was 1930, 1934Mather, 1936). Recombination values calculinked to Ms 1 (CLG 8) (R ϭ 24.8 Ϯ 1.2) and to W 1 (CLG 8) (R ϭ 36.4 Ϯ 1.3), and Y 11 was linked to Ms 1 (R ϭ 31.7 Ϯ 1.4). F 2 data lated from coupling data can differ significantly from suggested that Y 11 segregated independently of W 1 , while F 2:3 data those calculated from repulsion data (Butler, 1968; Imindicated the two were linked (R ϭ 38.4 Ϯ 3.2). Our data indicated mer, 1930, 1934 Mather, 1951). that CLGs 6 and 8 belong to the same linkage group, which is molecu-Weiss (1970) reported a recombination value of lar linkage group F (MLG F), and chromosome 13. Y 11 and Adh 1 are 12.1 Ϯ 0.7 between the Y 11 and Df 2 loci that established at the ends of the chromosome segment studied, and Y 23 is located soybean CLG 6. The first reported study involving loci between Ms 6 and St 5 . Recombination values among the other loci of of classical CLG 8 was by Palmer (1976), for Ms 1 and CLG 8, and between them and loci of other CLGs were consistent with W 1 . However, many of the soybean studies looked at published values. This information will be useful in the reassignment of CLGs, ordering of loci, and will enhance molecular genetic linkage linkage between two loci at a time. This manner of mapping in soybean. studying linkage can result in a range of significantly different map distances due to factors mentioned earlier. Variation in recombination values in soybean has been documented (Hildebrand et al.

In our previous Populus breeding, compatible crosses between P. maximowiczii A. Henry and P. deltoides Bartr. ex Marsh corroborated the potential of interspecific hybrids, despite low seed set. Our current objective was to test the range of incompatibility among intraspecific and interspecific crosses using parental germplasm from the sections Aigeiros Duby (P. deltoides and P. nigra L.) and Tacamahaca Spach (P. maximowiczii). We determined the success rate of crosses, along with seed production and seedling viability. The success of crosses ranged from complete incompatibility to complete compatibility, with 29% to 85% of the transplanted germinants developing into healthy seedlings.

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This research was challenging, but has greatly increased my understanding of genetics and ability to cope with challenging situations. Thanks to all my committee members, Drs.

Mapping mutants of classical linkage groups 6 and 8 (CLGs 6 and 8) in soybean [Glycine max (L.) Merr.] can enhance the identification of important agronomic traits. Genetic data suggest that CLGs 6 and 8 may belong to the same linkage group. Our objectives were to determine if CLGs 6 and 8 are the same or different linkage groups and to determine the gene order. Genotypes containing mutants of CLGs 6 and 8 and mutants of other CLGs were crossed in various combinations. Data for the different characters were collected from F2 populations and F2:3 families. Recombination values confirmed that CLG 6 characters, Df2 and Y11 were linked (R = 27.0 ± 5.9), Df2 was linked to Ms1 (CLG 8) (R = 24.8 ± 1.2) and to W1 (CLG 8) (R = 36.4 ± 1.3), and Y11 was linked to Ms1 (R = 31.7 ± 1.4). F2 data suggested that Y11 segregated independently of W1, while F2:3 data indicated the two were linked (R = 38.4 ± 3.2). Our data indicated that CLGs 6 and 8 belong to the same linkage group, which is molecular linkage group F (MLG F), and chromosome 13. Y11 and Adh1 are at the ends of the chromosome segment studied, and Y23 is located between Ms6 and St5 Recombination values among the other loci of CLG 8, and between them and loci of other CLGs were consistent with published values. This information will be useful in the reassignment of CLGs, ordering of loci, and will enhance molecular genetic linkage mapping in soybean.