Genetic diversity and population structure analysis in Perilla frutescens from Northern areas of China based on simple sequence repeats.

In this study, 21 simple sequence repeat (SSR) markers were used to evaluate the genetic diversity and population structure among 77 Perilla accessions from high-latitude and middle-latitude areas of China. Ninety-five alleles were identified with an average of 4.52 alleles per locus. The average polymorphic information content (PIC) and genetic diversity values were 0.346 and 0.372, respectively. The level of genetic diversity and PIC value for cultivated accessions of Perilla frutescens var. frutescens from middle-latitude areas were higher than accessions from high-latitude areas. Based on the dendrogram of unweighted pair group method with arithmetic mean (UPGMA), all accessions were classified into four major groups with a genetic similarity of 46%. All accessions of the cultivated var. frutescens were discriminated from the cultivated P. frutescens var. crispa. Furthermore, most accessions of the cultivated var. frutescens collected in high-latitude and middle-latitude areas were distinguished depending on their geographical location. However, the geographical locations of several accessions of the cultivated var. frutescens have no relation with their positions in the UPGMA dendrogram and population structure. This result implies that the diffusion of accessions of the cultivated Perilla crop in the northern areas of China might be through multiple routes. On the population structure analysis, 77 Perilla accessions were divided into Group I, Group II, and an admixed group based on a membership probability threshold of 0.8. Finally, the findings in this study can provide useful theoretical knowledge for further study on the population structure and genetic diversity of Perilla and benefit for Perilla crop breeding and germplasm conservation.

Bulk segregant analysis (BSA) for improving cold stress resistance in maize using SSR markers.

In this study, eight inbred maize lines with high or low tolerance to cold temperature were investigated using bulk segregant analysis (BSA). Genetic diversity and genetic relationships were investigated using 100 simple sequence repeat (SSR) markers linked to cold tolerance in maize. A total of 319 alleles were identified. Among these, 128 were high coldtolerant-specific alleles and 61 were poorly coldtolerant-specific alleles, while the remaining 130 were shared between the two types. The number of alleles per locus ranged from 2 to 5, with an average of 3.19. The major allele frequency varied from 0.39 to 0.53 with an average of 0.47. The average gene diversity and polymorphic information content among all lines were 0.63 and 0.58, respectively. A dendrogram analysis identified three main clusters and most of the high tolerant inbred lines were clearly distinguished from the poorly tolerant inbred lines. In addition to the BSA, a total of 84 SSR markers were identified as high cold tolerance-specific alleles and 52 SSRs were detected as poorly cold tolerance-specific alleles. Of these, bnlg1273, umc1124, dupssr21, mmc0251, mmc0181, and phi041 have great potential for being molecular markers for cold tolerance in maize. Our results were in agreement with results previously reported for SSR markers linked with cold tolerance in maize. The identification and characterization of high and poorly cold tolerant maize lines based on SSR markers will be useful for future maize breeding studies.

Analysis of the genetic diversity of super sweet corn inbred lines using SSR and SSAP markers.

In this study, we compared the efficiency of simple sequence repeat (SSR) and sequence specific amplified polymorphism (SSAP) markers for analyzing genetic diversity, genetic relationships, and population structure of 87 super sweet corn inbred lines from different origins. SSR markers showed higher average gene diversity and Shannon's information index than SSAP markers. To assess genetic relationships and characterize inbred lines using SSR and SSAP markers, genetic similarity (GS) matrices were constructed. The dendrogram using SSR marker data showed a complex pattern with nine clusters and a GS of 53.0%. For SSAP markers, three clusters were observed with a GS of 50.8%. Results of combined marker data showed six clusters with 53.5% GS. To analyze the genetic population structure of SSR and SSAP marker data, the 87 inbred lines were divided into groups I, II, and admixed based on the membership probability threshold of 0.8. Using combined marker data, the population structure was K = 3 and was divided into groups I, II, III, and admixed. This study represents a comparative analysis of SSR and SSAP marker data for the study of genetic diversity and genetic relationships in super sweet corn inbred lines. Our results would be useful for maize-breeding programs in Korea.

Non-parental banding patterns in recombinant inbred line population of maize with SSR markers.

We observed 3 types of non-parental banding patterns using simple-sequence repeat primers in a recombinant inbred line maize population developed from 2 inbred lines, Mo17 and KW7. We observed alleles that were not present in either of the parents, known as non-parental alleles. Although non-parental alleles are a consequence of genetic variation, they are less common in progenies derived from inbred lines. Generally, when non-parental alleles are encountered during genotyping analysis, they are either deleted from the analysis or considered to be missing data. However, before making a decision regarding how to treat non-parental alleles, it is important to understand the mechanism through which they form. There are a variety of potential reasons for the formation of non-parental bands, including recombination or mutation in the simple-sequence repeat region, residual heterozygosity in parental lines, or chromosomal aberrations resulting from rearrangements and transposons. In this article, we discuss the potential reasons behind the formation of the non-parental alleles observed in our data.

Genetic diversity, population structure, and association mapping of agronomic traits in waxy and normal maize inbred lines.

Understanding genetic diversity, population structure, and linkage disequilibrium is a prerequisite for the association mapping of complex traits in a target population. In this study, the genetic diversity and population structure of 40 waxy and 40 normal inbred maize lines were investigated using 10 morphological traits and 200 simple sequence repeat (SSR) markers. Based on a population structure analysis, the 80 maize inbred lines were divided into three groups: I, II, and admixed. Significant marker-trait associations were identified between the markers and the 10 morphological traits, which were studied according to the model used to confirm the association. Using a general linear model, the lowest R(2) value (9.03) was detected in umc1139, which was associated with ear number, and the highest (43.97) was in umc1858, which was associated with plant height. Using a mixed linear model, the lowest R(2) value (18.74) was in umc1279, which was associated with ear weight; the highest (27.66) was in umc1858, which was associated with 100-kernel weight. The SSR markers identified in the present study may serve as useful molecular markers for selecting important yield and agronomic traits. These results will be useful for marker-assisted selection in maize breeding programs, to help breeders choose parental lines and markers for crosses.

Genetic analysis of seed-shattering genes in rice using an F3:4 population derived from an Oryza sativa x Oryza rufipogon cross.

Seed shattering of wild plant species is thought to be an adaptive trait to facilitate seed dispersal. For rice breeding, seed shatter-ing is an important trait for improving breeding strategies, particularly when developing lines use interspecific hybrids and introgression of genes from wild species. We developed F3:4 recombinant inbred lines from an interspecific cross between Oryza sativa cv. Ilpoombyeo and Oryza rufipogon. In this study, we genetically analyzed known shat-tering-related loci using the F3:4 population of O. sativa/O. rufipogon. CACTA-AG190 was significantly associated with the shattering trait CACTA-TD according to bulked segregant analysis results, and was found in the qSH-1 region of chromosome 1. Fine genetic mapping of the flanking regions around qSH-1 based on CACTA-AG190 revealed multiple-sequence variations. The highest limit of detection based on quantitative trait locus analysis was observed between shaap-7715 and a 518-bp insertion site. Two other quantitative trait locus analyses of seed-shattering-related loci, qSH-4 and sh-h, were performed using simple sequence repeat and allele-pecific single nucleotide polymor-phism markers. Our results can be applied for rice-breeding research, such as marker-assisted selection between cultivated and wild rice.