국화(Chrysanthemum morifolium)는 다양한 화색과 화 형 때문에 세계에서 가장 인기 있는 관상식물 중 하나 로서 절화, 분화 및 화단용 등 다양한 형태의 국화에 대 한 요구가 증가하고 있다. 본 연구는 SSR 마커를 이용하 여 국화 60 품종에 대한 유전적 유연관계를 조사하고, 군 집분석결과와 표현형간의 상관관계를 조사하기 위하여 수 행하였다. 표현형질 38개를 이용한 군집분석 결과, 대부 분의 국화 품종들이 화형과 화색에 따라 8개의 그룹으 로 분류되는 것으로 나타났다. 본 연구에서 사용된 150 개의 SSR 프라이머는 기존연구에서 보고된 62개와 C. nankingense의 unigene 염기서열 및 C. morifolium의 EST 염기서열로부터 디자인한 88개로 구성되었다. 국화 8품종에 대한 다형성 및 banding pattern 결과를 토대로 하여 국화 60 품종의 DNA 증폭에 사용할 13개의 SSR 마커를 최종 선발하였다. SSR 마커를 이용하여 군집분석을 행한 결과, phylogenetic tree에서 국화 60 품종 전 부가 화색에 따라서 6개의 그룹으로 분류되는 것을 확 인할 수 있었다. Phylogenetic tree와 화색간의 상관관계 를 조사하기 위하여 화색을 종속변수, SSR 마커를 독립 변수로 설정한 다중회귀분석(MRA)을 행하였다. MRA 결 과는 화색과 SSR 마커간에 통계적 유의성이 높은 상관 관계(r2 = 0.903, P < 0.05)를 나타냈다. 본 연구결과는 경 쟁력 있는 국화 신품종 육종을 위한 데이터로 활용될 수 있을 것으로 생각된다.

Chrysanthemum (Chrysanthemum morifolium) is one of the most popular ornamental species in the world due to the great diversity of inflorescence form and color. There has been increasing demands for various types of chrysanthemums, such as cut flowers, potted plants and bedding plants. However, the genomic studies of this species have been not extensively conducted relative to other ornamental species due to high levels of polyploidy (2n = 4x =36 or 2n = 6x = 54) and heterozygosity as well as large genome size. In this work, we developed a molecular tool for cultivar identification using simple sequence repeats (SSRs) and investigated genetic diversity in 127 chrysanthemum cultivars. Of the 150 SSR primer pairs tested in this study, 62 primers were obtained from previous studies, while 88 primers were designed using the unigene sequences of C. nankingense and the Expressed Sequence Tag (EST) sequences of C. morifolium in the NCBI database. Thirty SSR primers were selected based on polymorphism and banding patterns in a subset of 8 cultivars and used to amplify the DNA of 127 chrysanthemum cultivars. The UPGMA dendrogram based on these 30 SSR markers showed that most of chrysanthemum cultivars were divided into five clusters. These results will benefit chrysanthemum research community to develop elite cultivars.

Cultivated tomato (Solanum lycopersicum L.) is an economically important vegetable and has a narrow genetic base due to intensive human selection through domestication and breeding. The low level of genetic variation between cultivated tomatoes has made it difficult to develop molecular markers for elite breeding lines. Recently, genome-wide 145,695 InDels were identified from in silico analysis of two tomato genome sequences, Heinz 1706 (S. lycoperiscum) and LA1589 (S. pimpnellifolium). Of these, 2,272 InDels were validated and 717 InDels showed polymorphism in cultivated tomatoes. In the present study, we selected 48 out of 717 InDels based on PIC value (> 0.3) and size (> 10 bp) to develop a DNA database for commercial tomato cultivars. We also used an additional set of 28 InDels that have been previously reported. These markers were distributed across 11 chromosomes with an average of 6.6 markers. A total of 48 F1 hybrid cultivars were collected from 20 seed companies and a subset of eight cultivars were used to test polymorphism of the InDel markers. The 37 InDel markers were polymorphic in these cultivars and were used to genotype additional 40 cultivars. Genetic distances and relationships between cultivars were assessed using the InDel genotypes of 48 cultivars. This analysis revealed that the InDel markers detected genetic variations to identify 46 cultivars. Our results demonstrate that the InDel markers will be a useful resource to construct a DNA database for tomato cultivars and to protect tomato breeder’s rights via variety identification.

Bacterial spot of tomato is a disease complex caused by at least four species of Xanthomonas and leads to severe yield and quality losses in humid growing conditions in the world. Five physiological species (T1-T5) have been defined by their virulence on tomato varieties. These races are associated with three species: X. euvesicatoria (T1), X. vesicatoria (T2), and X. perforans (T3-T5). Recent epidemics of X. gardneri has occurred in the Midwest United States. In this study, we developed germplasm with resistance to multiple species of bacterial spot. Six advanced breeding lines with at least three different source of resistance were crossed and their F1 hybrids were inter-mated to produce a complex breeding population consisting over 1,100 progeny. Three lines (OH7663, OH7667 and 2k7-6117-S2) were selected by field evaluations of the population against T1, T2, T3, and X. gardneri. Graphical genotypes demonstrated that these breeding lines contain a QTL and Rx-4/Xv3 in coupling phase on chromosome 11 as well as Rx-3 on chromosome 5. In order to test the combining ability of the lines, we developed hybrids from multiple crosses and conducted replicated field trials to evaluate bacterial spot resistance and yield. As a male parent, OH7663 showed acceptable combining ability for yield and for resistance against multiple species of Xanthomonas. Several hybrids produced yields that were not significantly different from yields of commercial varieties.

Bacterial spot of tomato (Solanum lycopersicum L.) is caused by at least four species of Xanthomonas with multiple physiological races. In this study, we developed a mapping population for association analysis of bacterial spot resistance. For this population, six advanced breeding lines with distinct sources of resistance were first crossed in all combinations and their F1 hybrids were intercrossed. The 1,100 segregating progeny from these crosses were evaluated in the field against T1 strains. Based on this individual evaluation, we selected 5% of the most resistant and 5% of the most susceptible progeny for evaluation as plots in two subsequent replicate field trials inoculated with T1 and T3 strains. A total of 461 markers across 12 chromosomes were used for genotyping these selections. Of these markers, an optimized subset of 384 SNPs was derived from the 7,720 SNP Infinium array developed by the Solanaceae Coordinated Agricultural Project (SolCAP). For association analysis to detect known resistance loci and additional novel loci, we used the mixed models with correction for population structure, and found that accounting for kinship appeared to be sufficient. Detection of known loci was not improved by adding a correction for structure using either a Q matrix from model-based clustering or covariate matrix from Principal Component Analysis. Both single-point and haplotype analyses identified strong associations in the region of the genome known to carry Rx-3 (chromosome 5) and Rx-4/Xv3 (chromosome 11). Additional QTL associated with resistance were detected on chromosomes 1, 3, 4, 6 and 7 for T1 resistance and chromosomes 2, 4, and 6 for T3 resistance. Haplotype analysis improved our ability to trace the origin of positive alleles. These results demonstrate that both known and novel associations can be identified using complex breeding populations that have experienced directional selection.