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Background: Anther culture has advantage to obtain a homozygous progeny by induced doubling of haploid chromosomes and to improve selection efficiency for invaluable agronomical traits. Therefore, anther culturing is widely utilized to breed new varieties and to induce genetic variations in several crops including rice. Genome sequencing technologies allow the detection of a massive number of DNA polymorphism such as SNPs and Indels between closely related cultivars. These DNA polymorphisms permit the rapid identification of genetic diversity among cultivars and genomic locations of heritable traits. To estimate sequence diversity derived from anther culturing, we performed whole-genome resequencing of five Korean rice accessions, including three anther culture lines (BLB, HY-04 and HY-08), their progenitor cultivar (Hwayeong), and an additional japonica cultivar (Dongjin).

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The National Agricultural Biotechnology Information Center (NABIC) reconstructed an AllergenPro database for allergenic proteins analysis and allergenicity prediction. The AllergenPro is an integrated web-based system providing information about allergen in foods, microorganisms, animals and plants. The allergen database has the three main features namely, (1) allergen list with epitopes, (2) searching of allergen using keyword, and (3) methods for allergenicity prediction. This updated AllergenPro outputs the search based allergen information through a user-friendly web interface, and users can run tools for allergenicity prediction using three different methods namely, (1) FAO/WHO, (2) motif-based and (3) epitope-based methods. AvailabilityThe database is available for free at http://nabic.rda.go.kr/allergen/

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Plant Breed. Biotech. 2015 (September) 3(3):208~215 http://dx.ABSTRACT Closely-related cultivars generally used for crossing in breeding lack sufficient known DNA polymorphisms with already developed DNA markers even though they exhibit remarkable phenotype difference. However, next-generation sequencing (NGS) enables the identification of massive DNA polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) between highly homologous genomes. This study conducted a whole-genome re-sequencing of two Korean japonica rice varieties, Junam and Nampyeong. The sequencing yielded 16.6 × 10 9 bps for Junam, and 15.1 × 10 9 bps for Nampyeong. After quality trimming and read mapping onto the reference genome sequence of Nipponbare, 11.9 × 10 9 bps from Junam and 10.6 × 10 9 bps from Nampyeong were mapped onto the reference sequence. The final effective mapping depth was 31.98x for Junam and 28.41x for Nampyeong. This study found 398,123 DNA polymophisms between Junam and Nampyeong. These were classified into 352,478 SNPs (88.5%) and 45,645 InDels (11.5%) by polymorphism types, 338,485 homozygous (85%) and 59,638 (15%) heterozygous by zygosity, and 331,855 intergenic (83.4%) and 66,268 genic (16.6%) by genomic location. To see the availability of these results in DNA marker development, Cleaved Amplified Polymorphic Sequences (CAPS) markers were developed based on 22 SNPs lying in restriction enzyme sites. Among them, 17 CAPS markers showed polymorphisms between Junam and Nampyeong. It is expected that sufficient DNA markers for mapping genes/QTLs with progeny population from a cross between Junam and Nampyeong can be developed based on the results of the study.

The next generation sequencing (NGS) has been developed rapidly in recent years, paving ways of discovering vast sequence variations among germplasms. Whole-genome sequencing was performed on the genomic DNA of Milyang23 and Gihobyeo using NGS and developed new CAPS (cleaved amplified polymorphic sequence) markers based on the single nucleotide polymorphisms (SNPs) in coding sequence between these varieties. The NGS sequencing yielded sequences of 60x coverage of the Nipponbare reference genome on average. A molecular genetic map was constructed with the recombinant inbred population derived from Milyang23/Gihobyeo cross (MGRIL) integrating the newly developed 146 CAPS makers and previously reported 219 PCR-based DNA markers. This map was applied to the detection of quantitative trait loci (QTLs) for stem internode diameters, culm length and panicle length in rice with MGRIL population. A total of 4 new QTLs were detected for stem diameter traits including the first internode diameter (I1D), second internode diameter (I2D), third internode diameter (I3D), and fourth internode diameter (I4D). Among stem diameter QTLs, qI1D5 had relatively 6.09 LOD (likelihood of odds) score and explained 8.99% of total variation. Only very small portion of SNPs through re-sequencing were used in this study. Much more markers can be developed by using SNP information acquired in this study, which will enable construction of high-density genetic map and more accurate QTL analysis of important agronomical traits with MGRIL population. This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. 서 언 작물 육종에 있어서 농업적으로 중요한 형질들은 독립적인 단일 유전자가 아니라 전체 염색체 상에 존재하는 수많은 유 전자들에 의해서 조절되는 양적형질이다. 따라서 오늘날은 이 러한 양적형질 유전자좌를 연구하기 위해서 고밀도 분자유전 지도 작성을 통해 유전자를 찾고, 그 기능을 밝히는 등의 접 근이 많이 이루어지고 있다(Li et al. 2011, Ookawa et al. 2010). 현재까지 고밀도 분자유전지도를 작성하기 위해 RFLP (restriction fragment-length polymorphism), RAPD (randomly amplified polymorphism) 및 AFLP (amplified fragment length polymorphism) 등 다양한 DNA 마커가 개발되었다. 벼에서는 자포니카 품종인 Nipponbare와 인디카 품종인 Kasalath 교배 후대 F2집단을 활용하여 2,275개 RFLP 마커들로 구성된 고 밀도 분자유전지도를 작성한 바가 있고(Harushima et al. 1998), 이는 벼 유전체 해독 프로젝트(International Rice Genome Sequencing Project, 2005)에 활용되기도 하였다. 기존의 DNA 마커들은 식별방법이 간편하지 못하고, 고비 용과 많은 소요시간이 걸린다. 게다가 출현빈도가 낮다는 한