Agromorphological traits dataset of butterfly pea accessions from Thailand, Indonesia, and Brazil.

Butterfly pea (Clitoria ternatea L.) is a horticultural crop also known as underutilized crop. All parts of the butterfly pea can be used into various products including flowers that can be used as natural dyes and traditional medicines. Besides that, the plant parts can be used as fodder and cover crop. The development of butterfly pea in Indonesia is still very low both in cultivation and utilization. Therefore, a breeding program is required to increase usefulness of butterfly pea can be done for the development. To assemble superior varieties of butterfly pea, it is necessary to determine the genetic diversity of both in agronomy and morphology. Genetic diversity and relationships are needed to evaluate plant germplasm. Raw data analysis was conducted after standardization using Principal Componet Analysis (PCA) and Hierarchical Clustering Analysis (HCA) to determine phenotypic diversity and relationship among the newly collected genetic resources. The data in this article showed broad phenotypic diversity with weight of fresh flower per plant, seed color, weight of total seed, pod width, calix length, flower color, petal number, number of total pods, plant height, number of seed per pod, weight total fresh flower, seed width, weight of fresh flower per plant, and seed length as distinguishing traits among the accessions. PCA based on agromorphogical traits showed eigenvalue ranged from 1.13 to 9.47 with a cumulative contribution of 93.02%. HCA showed butterfly pea accessions divided into two cluster with euclidean distance 0.27-4.65.

Pathotype Diversity of Phytophthora sojae in Eleven States in the United States.

Pathotype diversity of Phytophthora sojae was assessed in 11 states in the United States during 2012 and 2013. Isolates of P. sojae were recovered from 202 fields, either from soil samples using a soybean seedling bioassay or by isolation from symptomatic plants. Each isolate was inoculated directly onto 12 soybean differentials; no Rps gene or Rps 1a, 1b, 1c, 1k, 3a, 3b, 3c, 4, 6, 7, or 8. There were 213 unique virulence pathotypes identified among the 873 isolates collected. None of the Rps genes were effective against all the isolates collected but Rps6 and Rps8 were effective against the majority of isolates collected in the northern regions of the sampled area. Virulence toward Rps1a, 1b, 1c, and 1k ranged from 36 to 100% of isolates collected in each state, while virulence to Rps6 and Rps8 was less than 36 and 10%, respectively. Depending on the state, the effectiveness of Rps3a ranged from totally effective to susceptible to more than 40% of the isolates. Pathotype complexity has increased in populations of P. sojae in the United States, emphasizing the increasing importance of stacked Rps genes in combination with high partial resistance as a means of limiting losses to P. sojae.

A new integrated genetic linkage map of the soybean.

A total of 391 simple sequence repeat (SSR) markers designed from genomic DNA libraries, 24 derived from existing GenBank genes or ESTs, and five derived from bacterial artificial chromosome (BAC) end sequences were developed. In contrast to SSRs derived from EST sequences, those derived from genomic libraries were a superior source of polymorphic markers, given that the mean number of tandem repeats in the former was significantly less than that of the latter ( P<0.01). The 420 newly developed SSRs were mapped in one or more of five soybean mapping populations: "Minsoy" x "Noir 1", "Minsoy" x "Archer", "Archer" x "Noir 1", "Clark" x "Harosoy", and A81-356022 x PI468916. The JoinMap software package was used to combine the five maps into an integrated genetic map spanning 2,523.6 cM of Kosambi map distance across 20 linkage groups that contained 1,849 markers, including 1,015 SSRs, 709 RFLPs, 73 RAPDs, 24 classical traits, six AFLPs, ten isozymes, and 12 others. The number of new SSR markers added to each linkage group ranged from 12 to 29. In the integrated map, the ratio of SSR marker number to linkage group map distance did not differ among 18 of the 20 linkage groups; however, the SSRs were not uniformly spaced over a linkage group, clusters of SSRs with very limited recombination were frequently present. These clusters of SSRs may be indicative of gene-rich regions of soybean, as has been suggested by a number of recent studies, indicating the significant association of genes and SSRs. Development of SSR markers from map-referenced BAC clones was a very effective means of targeting markers to marker-scarce positions in the genome.

Introgression of a quantitative trait locus for yield from Glycine soja into commercial soybean cultivars.

The value of exotic germplasm in broadening the genetic base of most crops has been demonstrated many times. However, the difficulties involved in working with exotic germplasm have limited their utility in plant breeding. Unwanted linkages often thwart the successful incorporation of beneficial exotic genes into commercial lines. Thus, the use of exotics in traditional breeding makes the process of crop improvement a tedious, time-consuming and expensive endeavor. The availability of molecular markers makes it possible to isolate specific genomic regions and transfer them into commercial varieties with minimal linkage drag. We found a yield-enhancing quantitative trait locus (QTL) from Glycine soja (Siebold and Zucc.) by evaluating a population of 265 BC(2) individuals from a cross between HS-1 and PI 407305. The yield QTL was located on linkage group B2(U26) of the soybean [Glycine max (L.) Merrill] genetic linkage map. In a 2-year, multi-location study, individuals carrying the PI 407305 haplotype at the QTL locus demonstrated a 9.4% yield advantage over individuals that did not contain the exotic haplotype. When tested in a more uniform "HS-1-like" background in two locations, we observed an 8% yield advantage for lines that carry the PI 407305 haplotype. We further assessed the QTL effect in various elite soybean genetic backgrounds. The yield effect was consistently observed in only two of six genetic backgrounds. Individuals carrying the PI 407305 haplotype at the QTL locus had a 9% yield advantage in yield trials across locations. Despite the limited adaptability of this yield-QTL across genetic backgrounds, this study demonstrates the potential of exotic germplasm for yield enhancement in soybean.

Genome duplication in soybean (Glycine subgenus soja).

Restriction fragment length polymorphism mapping data from nine populations (Glycine max x G. soja and G. max x G. max) of the Glycine subgenus soja genome led to the identification of many duplicated segments of the genome. Linkage groups contained up to 33 markers that were duplicated on other linkage groups. The size of homoeologous regions ranged from 1.5 to 106.4 cM, with an average size of 45.3 cM. We observed segments in the soybean genome that were present in as many as six copies with an average of 2.55 duplications per segment. The presence of nested duplications suggests that at least one of the original genomes may have undergone an additional round of tetraploidization. Tetraploidization, along with large internal duplications, accounts for the highly duplicated nature of the genome of the subgenus. Quantitative trait loci for seed protein and oil showed correspondence across homoeologous regions, suggesting that the genes or gene families contributing to seed composition have retained similar functions throughout the evolution of the chromosomes.

Targeted comparative genome analysis and qualitative mapping of a major partial-resistance gene to the soybean cyst nematode.

A major partial-resistance locus to the soybean cyst nematode (Heterodera glycines Ichinohe; SCN) was identified on linkage group 'G' of soybean [Glycine max (L.) Merr.] using restriction fragment length polymorphisms (RFLPs). This locus explained 51.4% (LOD=10.35) of the total phenotypic variation in disease response in soybean Plant Introduction (PI) 209332, 52.7% (LOD=15.58) in PI 90763, 40.0% (LOD=10.50) in PI 88788, and 28.1% (LOD=6.94) in 'Peking'. Initially, the region around this major resistance locus was poorly populated with DNA markers. To increase marker density in this genomic region, first random, and later targeted, comparative mapping with RFLPs from mungbean [Vigna radiata (L.) R. Wilcz.] and common bean (Phaseolus vulgaris L.) was performed, eventually leading to one RFLP marker every 2.6 centimorgans (cM). Even with this marker density, the inability to resolve SCN disease response into discrete Mendelian categories posed a major limitation to mapping. Thus, qualitative scoring of SCN disease response was carried out in an F5∶6 recombinant inbred population derived from 'Evans'xPI 209332 using a 30% disease index cut-off for resistance. Using the computer program JoinMap, an integrated map of the region of interest was created, placing the SCN resistance locus 4.6 cM from RFLP marker B53 and 2.8 cM from Bng30. This study demonstrates how a combination of molecularmapping strategies, including comparative genome analysis, join mapping, and qualitative scoring of a quantitative trait, potentially provide the necessary tools for high-resolution mapping around a quantitative-trait locus.