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>

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.

Development of Near Isogenic Lines to Investigate Hybrid Sterility Genes in Interspecific Crosses Rice

Reflinur,Joong Hyoun Chin,Tae Ho Ham,Sang Ho Chu,Ho Hoon Lee,Hee Jong Koh 한국육종학회 2008 한국육종학회 학술발표회 발표요지 Vol.40 No.1

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

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.

Identification of Quantitative Trait Loci for Agronomic Traits in Two Rice Populations Derived from a Cross with a Wide Compatibility Line

( Jeong Hwan Seo ),( Reflinur ),( Sung Han Kim ),( Mi Ok Woo ),( Hee Jong Koh ) 한국육종학회 2014 Plant Breeding and Biotechnology Vol.2 No.3

Hybrid sterility is the major obstacle that can act as a barrier to genetic recombination and limits favorable gene transfer during inter-subspecific crosses in rice. However, hybrid sterility can be overcome by utilization of wide-compatible varieties (WCV). In the present study, two F2 populations generated from crosses between a wide-compatibility line (HWC-line) and two Korean varieties, Dasan and Hwacheong were evaluated for eight agronomic traits. A total of 157 molecular markers consisted of 116 STS, 40 SSR and 1 FNP were used to create genetic linkage maps spanning all 12 chromosomes. Twenty-one main-effect QTLs (M-QTLs) were identified in HWC-line/Dasan (HD) population. These loci are populated with two QTLs for culm length, one for spikelet per panicle, one for spikelet fertility, four for grain length, five for grain width, five for grain shape, and three for 100 grain-weight. In HWC-line/Hwacheong (HH) population, 17 QTLs were detected including two QTLs for culm length, one for panicle length, one for spikelet fertility, five for grain length, three for grain width, three for grain shape, and two for 100-grain weight. Of the total 34 QTLs found in the two F2 populations, 9 QTLs associated with culm length, grain length, grain width and grain shape were newly identified in this study. These QTLs will be useful for further understanding the genetic basis of agronomic traits and for developing markers for selection in rice breeding. In addition, HWC-line could be used as a bridge for inter-subspecies crosses overcoming hybrid sterility.

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.

Identification of QTLs for hybrid fertility in inter-subspecific crosses of rice (Oryza sativa L.)

진중현,추상호,Wenzhu Jiang,Young-Il Cho,Reflinur Basyirin,Darshan S. Brar,고희종 한국유전학회 2011 Genes & Genomics Vol.33 No.1

Two subspecies in rice, japonica and indica, have their own ecotypic traits. However, reproductive barriers such as spikelet sterility in hybrid progenies between subspecies have been an obstacle in breeding programs for combining desirable traits from both subspecies through inter-subspecific hybridization. The 166 F_9 RILs and two BC_1F_(1s)’ were analyzed for spikelet and pollen fertility with the parents and F_1 between Dasanbyeo (DS, indica) / TR22183 (TR, japonica). A frame map was constructed using a total of 218 polymorphic STS and SSR markers. In both BC1F1s’ of DS//DS/TR and TR//DS/TR, clusters of significant QTLs for spikelet and pollen fertility were identified on the short arm of chromosome 5 and chromosome 8. Nine and ten digenic epistatic interactions for DS//DS/TR and TR//DS//TR were identified,respectively. HF-QTLs were detected at the similar position with subspecies-specific markers and segregation distortion loci, implying that HF-QTLs might be associated with the differentiation of indica and japonica. Hybrid fertility/sterility and its relationship with other traits are discussed in relation to the reproductive barriers between subspecies of rice.

Genetic diversity of mungbean (<i>Vigna radiata</i> L.) germplasm in Indonesia

Lestari, Puji,Kim, Sue Kyung,Reflinur,,Kang, Yang Jae,Dewi, Nurwita,Lee, Suk-Ha Cambridge University Press 2014 Plant genetic resources Vol.12 No.1

<P>Despite widespread mungbean [<I>Vigna radiata</I> (L.) Wilczek] consumption in Indonesia, few molecular studies have been carried out on accessions and available data are minimal. In this study, we used 30 newly developed simple sequence repeat (SSR) markers designed from the mapped sequence scaffolds of the Korean Sunhwanokdu and Gyeonggijaerae 5 mungbean genomes. These markers were used to examine loci in 83 mungbean accessions collected from diverse geographical areas in Indonesia. A total of 107 alleles were detected among the accessions with 29 polymorphic markers. However, the mean of polymorphic information content (0.33) value and diversity index (0.38) value was indicative of low genetic diversity in this germplasm. The mungbean population structure was not clearly differentiated and the number of subpopulations was unclear. Neighbour-joining tree analysis revealed that the genetic cluster did not reflect the geographical origin of the accessions. Interestingly, the most agriculturally improved varieties were genetically similar to some landraces from one of the main mungbean-producing regions. These newly developed SSR markers could be useful for detecting genetic variability as a basis for establishing a conservation strategy for mungbean germplasm with the aim of enhancing Indonesian breeding programmes.</P>

Mapping Quantitative Trait Loci Conferring Blast Resistance in Upland Indica Rice (Oryza sativa L.)

Puji Lestari,Masdiar Bustamam,Kurniawan Rudi Trijatmiko,Reflinur,Ahmad Warsun,Tasliah,Isabelita Ona,Casiana Vera Cruz 한국작물학회 2011 Journal of crop science and biotechnology Vol.14 No.1

A genetic analysis of blast resistance in upland rice variety is very crucial. In this study, we performed a linkage mapping of quantitative trait loci (QTLs) for blast resistance using an advanced backcross population from a cross between Way Rarem (susceptible indica variety) and Oryzica Llanos 5 (durable resistant indica variety). A transgressive segregation was observed in the advanced backcross population of Way Rarem//Oryzica Llanos 5. A total of 16 QTLs have been identified along chromosomes 1, 3, 5, 6, 7, 8,9, and 11 against eight blast pathogen isolates. Each QTL accounted from 11.31 to 45.11% of the variation in blast resistance. Most QTLs showed race specificity, demonstrating the small effect of such QTLs. Unexpectedly, several superior blast resistance alleles were contributed by Way Rarem, the susceptible-recurrent parent. Among eight candidate defense response genes detected in several loci, a single gene (oxalate oxidase) present on chromosome 3 was found to be associated with blast resistance in upland indica rice. Ultimately, these advanced backcross lines with resistance to blast tagged by markers might be useful for pyramiding blast resistance alleles in upland rice.