Characterization and mapping of d13, a dwarfing mutant gene, in rice

Md. Babul Akter,Rihua Piao,Reflinur,Md. Lutfor Rahman,이윤주,서정환,김백기,고희종 한국유전학회 2015 Genes & Genomics Vol.37 No.11

Plant height is one of the most important agronomic traits in crop breeding because dwarf and semidwarf cultivars are resistant to lodging and have led to remarkable yield increases in cereal crops. Although several genes related to gibberellins signaling or biosynthesis resulting in dwarfism have been isolated, however, lots of causal genes controlling dwarfism remain to be uncovered. We characterized a dwarf mutant (ID13) in rice. The mutant displayed several altered phenotypes compared to the wild type, such as reduced plant height, increased tiller number, short and rounded leaf tips, presence of a yellowish stripe on the leaf blade, late and asynchronous heading, strong root systems, short erect panicle, smaller seed size, etc. The dwarfism of the mutant was responsive to gibberellic acid (GA), based on the analyses of two GAmediated processes. Anatomical observations revealed that the mutant plants had fewer vascular bundles and reduced cell size compared with wild type plants. Genetic analysis indicated that the dwarf mutant was controlled by a single recessive gene, d13, which was flanked by two STS markers, DMR-3 and S5789, within the physical distance of 265 kb around the centromeric region on chromosome 9. Cloning and functional analysis is in progress.

Fine mapping and candidate gene analysis of a new mutant gene for panicle apical abortion in rice

Md. Babul Akter,Rihua Piao,Backki Kim,Yunjoo Lee,Eunbyeol Koh,Hee-Jong Koh 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07

The architecture of rice panicle is primarily determined by the arrangement of branches and spikelets, and it directly affects grain yield. We identified a mutant for panicle apical abortion from a japonica cultivar Hwacheongbyeo treated with N-methyl-N-nitrosourea. Under normal growth conditions, the mutant had multiple abnormal phenotypes, such as a slight reduction in plant height, narrow and dark green leaf blades, and small erect panicles with clear panicle apical abortion compared to the wild-type plants. Genetic analysis revealed that the panicle apical abortion was controlled by a single recessive gene, which is tentatively designated as paa. The paa gene was fine mapped at an interval of 71 kb flanked by STS markers aptn3 and S6685-1 at the long arm of chromosome 4. Sequence analysis of the candidate genes within the delimited region showed a single base-pair change corresponding to an amino acid substitution from glycine to glutamic acid. We expect that the paa gene will be a clue to uncover the molecular mechanism of panicle apical abortion and to maintain the panicle identity for grain yield in rice breeding programs.

Fine mapping and candidate gene analysis of a new mutant gene for panicle apical abortion in rice

Akter, Md. Babul,Piao, Rihua,Kim, Backki,Lee, Yunjoo,Koh, Eunbyeol,Koh, Hee-Jong Springer-Verlag 2014 Euphytica Vol.197 No.3

Development of a SNP genotyping set for rice genetic analysis and molecular breeding using the Fluidigm platfo

Jeonghwan Seo,Md. Babul Akter,Yoon Kyung Lee,Hee-Jong Koh 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

Single nucleotide polymorphisms (SNPs) are the most abundant variation in plant genomes. As DNA markers, SNPs are rapidly replacing simple sequence repeats (SSRs) and sequence tagged sites (STSs) markers, because SNPs are more abundant, stable, easy to automation, efficient, and increasingly cost-effective. We developed a 96-plex indica/japonica SNP genotyping set for genetic analysis and molecular breeding in rice using Fluidigm platform. Informative SNPs for indica/japonica populations were selected from 1536 Illumina SNPs and 44K Affymetrix SNP chip data of Rice Diversity and our resequencing data sets. Selected SNPs were evenly distributed across 12 chromosomes and average physical distance between adjacent SNP markers was 4.38Mb. We conducted genetic diversity analysis of 49 Bangladesh germplasm and check varieties to test a 96-plex indica/japonica SNP genotyping set we developed. High-throughput Fluidigm SNP genotyping system will serve a more efficient and valuable tool for genetic diversity analysis, DNA fingerprinting, quantitative trait locus (QTL) mapping and background selection for crosses between indica and japonica in rice. This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ008125), Rural Development Administration, Republic of Korea.

Identification of QTLs Associated with indica-japonica Differentiation-Related Traits in Rice (Oryza sativa L.)

( Reflinur ),( Backki Kim ),( Puji Lestari ),( Md Babul Akter ),( Hee-jong Koh ) 한국육종학회 2018 Plant Breeding and Biotechnology Vol.6 No.3

Understanding the morphological and physiological characteristics which are attributable to determine indica and japonica subspecies of Asian rice (Oryza sativa L.) is important to conceive breeding strategy. However, information of quantitative trait loci (QTLs) associated with targeted traits related to subspecies domestication and differentiation-related traits remains limited. Two reciprocal F2 mapping populations generated from a cross between Ilpumbyeo (japonica) and Dasanbyeo (indica) were developed and used for constructing genetic maps to identify QTLs responsible for subspecies specific-related traits using 107 sequence-tagged site (STS) markers. A total of 26 main-effect QTLs for subspecies-related traits such as grain length, grain width, grain length-width ratio, apiculus hair length, and potassium chlorate resistance, were detected on seven chromosomes (1, 2, 3, 4, 5, 6, and 8). Of the detected QTLs, 14 QTLs corresponding to the previously reported QTLs suggesting the functional conservation of QTLs across populations and the remaining 12 QTLs appeared to be novel QTLs. A total of 29 significant epistatic QTLs were also detected in present study demonstrating an important genetic basis of epistatic interactions for complex subspecies-related traits. These results suggest that the subspecies-related traits and detected QTLs should be taken into consideration to incorporate with marker-assisted selection strategy in rice breeding program.

Analysis of segregation distortion and its relationship to hybrid barriers in rice

Reflinur,Kim, Backki,Jang, Sun Mi,Chu, Sang-Ho,Bordiya, Yogendra,Akter, Md Babul,Lee, Joohyun,Chin, Joong Hyoun,Koh, Hee-Jong Springer New York 2014 Rice Vol.7 No.-

<P><B>Background</B></P><P>Segregation distortion (SD) is a frequently observed occurrence in mapping populations generated from crosses involving divergent genotypes. In the present study, ten genetic linkage maps constructed from reciprocal F<SUB>2</SUB> and BC<SUB>1</SUB>F<SUB>1</SUB> mapping populations derived from the parents Dasanbyeo (<I>indica</I>) and Ilpumbyeo (<I>japonica</I>) were used to identify the distribution, effect, and magnitude of the genetic factors underlying the mechanisms of SD between the two subspecies.</P><P><B>Results</B></P><P>SD loci detected in the present study were affected by male function, female function, and zygotic selection. The most pronounced SD loci were mapped to chromosome 3 (transmitted through male gametes), chromosome 5 (transmitted through male gametes), and chromosome 6 (transmitted through female gametes). The level of SD in BC<SUB>1</SUB>F<SUB>1</SUB> populations which defined by chi-square value independence multiple tests was relatively low in comparison to F<SUB>2</SUB> populations. Dasanbyeo alleles were transmitted at a higher frequency in both F<SUB>2</SUB> and BC<SUB>1</SUB>F<SUB>1</SUB> populations, suggesting that <I>indic</I> a alleles are strongly favored in inter-subspecific crosses in rice. SD loci in the present study corresponded to previously reported loci for reproductive barriers. In addition, new SD loci were detected on chromosomes 2 and 12.</P><P><B>Conclusion</B></P><P>The identification of the distribution of SD and the effect of genetic factors causing SD in genetic mapping populations provides an opportunity to survey the whole genome for new SD loci and their relationships to reproductive barriers. This provides a basis for future research on the elucidation of the genetic mechanisms underlying SD in rice, and will be useful in molecular breeding programs.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12284-014-0003-8) contains supplementary material, which is available to authorized users.</P>

QTLs for hybrid fertility and their association with female and male sterility in rice

Reflinur,Backki Kim,Joong Hyoun Chin,Sun Mi Jang,Babul MD Akter,Joohyun Lee,Hee-Jong Koh 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07

Hybrid sterility is one of the major barrier to the application of wide crosses in plant breeding and is commonly encountered in crosses between indica and japonica rice varieties. Ten mapping populations comprised of two reciprocal F2 and eight BC1F1 populations generated from the cross between Ilpumbyeo (japonica) and Dasanbyeo (indica) were used to identify QTLs and to interpret the gametophytic factors involved in hybrid fertility or sterility between two subspecies. Frame maps were constructed using a total of 107 and 144 STS markers covering 12 rice chromosomes in two reciprocal F2 and eight BC1F1 populations, respectively. A total of 15 main-effect QTLs and 17 significant digenic- epistatic interactions controlling spikelet fertility (SF) were resolved in the the entire genome map of F2 BC1F1 populations . Among detected QTLs responsible for hybrid ferility, four QTLs, qSF5.1 and and qS F5.2 on chromosome 5, qSF6.2 on chromosome 6, and qSF12.2 on chromosome 12 were identified as major QTLs since they were located at corresponding position in at least three mapping populations. Loci qSF5.1, qSF6.1 and qSF6.2 were responsible for both female and male sterility, whereas qSF3.1, qSF7 and qSF 12.2 affected the spikelet fertility only through embryosac factors, and qSF9.1 did through pollen factors. Five new QTLs identified in this study will be helpful for understanding the hybrid sterility and for breeding programs via inter-subspecific hybridization.

Preliminary Studies of Molecular Mechanism of Hybrid Sterility Genes in Inter-subspecific Crosses in Rice

Reflinur Basyirin,Koong Hyoun Chin,Jung Hyun Park,Sang Ho Chu,Baek Ki Kim,Tae Ho Ham,Md Babul Akter,Hee Jong Koh 한국육종학회 2009 한국육종학회 학술발표회 발표요지 Vol.41 No.1