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Marker Assisted Selection-A New Paradigm in Plant Breeding
Kshirod K. Jena,Huhn Pal Moon,David J. Mackill 한국육종학회 2003 한국육종학회지 Vol.35 No.3
The production and productivity of major crop plants have reached their plateu during the past decade because of adop-tion of green revolution technologies. However, further increase in production of cereals with improved cereal quality is imperativeto fe
Effectiveness of marker-assisted backcrossing breeding for biotic resistance in rice
Jung-Pil Suh,Kshirod K. Jena,Young-Chan Cho,Ji-Ung Jeung,Yong-Jae Won,Im-Soo Choi,Jeom-Ho Lee,Myeong-Ki Kim,Chung-Kon Kim 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
The transfer of a biotic resistance gene from indica rice cultivars into japonica cultivars by conventional breeding methods often difficult due to high sterility of the progenies, poor plant type, and linkage drag. Molecular markers provide opportunities to map resistance genes and accelerate the application of marker-assisted backcross(MAB) breeding through the precise transfer of target genomic regions into the recurrent parent. The basis of MAB breeding is to transfer a specific gene/allele of the donor parent into the recurrent parent genome while selecting against donor introgressions across the rest of the genome. The effectiveness of MAB breeding depends on the availability of closely linked DNA markers for the target locus, the size of the population, the number of backcrosses and the position and number of markers for background selection. We have successfully developed Bph18 version of the commercially cultivated japonica elite cultivar by using MAB and incorporating the resistance gene Bph18 that conferred enhanced resistance to BPH. MAB breeding provides a new opportunity for the selective transfer of biotic resistance genes into elite indica rice cultivars devoid of linkage drag. In additon, molecular markers precisely estimate the introgression of chromosome segments from donor parents and can speed up the recipient genome recovery via background selection.
A simple, rapid, and high-throughput DNA extraction method for PCR analysis from rice plants
Sung-Ryul Kim,Gynheung An,Kshirod K Jena 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
Polymerase chain reaction (PCR) is highly utilized for QTL analysis, positional cloning of valuable genes, and molecular breeding in crop science. Usually those experiments handle DNA samples of many genotypes (up to several thousands). However, many DNA extraction protocols require longer time using harmful chemicals such as chloroform, phenol, and liquid nitrogen. Here, we introduce a new DNA extraction method for PCR with agarose/PAGE analysis from a diversity panel of rice genotypes identified with yield enhancing traits. This protocol consists of four steps including injection of extraction buffer (20 mM Tris-HCl pH9.5, 200 mM KCl, 2 mM EDTA) into the tubes containing leaf tissues and steel balls, and crushing tissues using Geno-Grinder without liquid nitrogen, sample incubation at 65°C, and then centrifugation for removing cell debris. After centrifugation the crude extracts directly used as template DNA for PCR. Through this protocol we could complete F1 hybridity test from approximately 2,100 plants that come from 96 cross combinations with 13 SSR markers. In addition, we tested the DNA quality by PCR amplification of high GC-rich region and large target size (-2kb). From these results our DNA extraction method produces enough DNA quality for PCR and is suitable for large scale molecular analysis from rice plants.
( Sung Ryul Kim ),( Jungil Yang ),( Gynheung An ),( Kshirod K Jena ) 한국육종학회 2016 Plant Breeding and Biotechnology Vol.4 No.1
Preparation of DNA is cumbersome especially in the case of large numbers of plant samples. Several simple plant DNA preparation methods have been developed for use in conjunction with polymerase chain reaction (PCR) analysis. However, those methods have not been adopted widely for rice molecular analysis. We present a new, simple, and inexpensive method using tris-phosphate (TPE) ethylenediaminetetraacetic acid (EDTA) buffer (100 mM tris-HCl pH9.5, 1 M KCl, 10 mM EDTA pH 8.0) without phenol-chloroform extraction and DNA precipitation steps. The method consists of five steps: leaf tissue grinding, incubating in TPE buffer at 65oC for 20 to 90 minutes, diluting extracts with water, centrifuging to sediment tissue debris, and transferring the supernatant for direct use in PCR or storage. Agarose gel analysis of the crude extracts indicated that the method produced intact genomic DNA (gDNA) from young and old leaves of both young seedlings and mature plants. Leaf sample size (0.5 to 8.0 cm long) for DNA preparation was less sensitive to PCR than the previous methods. DNA quality was tested through PCR amplification of various GC content regions and product sizes, and we obtained bands from all samples, indicating that the method produced suitable DNA quality for PCR. gDNAs were stable for longer than eight months at 4oC. This protocol enabled one person to handle several hundred samples in a day and was tested through various PCR-gel analyses such as genotyping of rice T-DNA mutant lines, positional cloning of rice mutant, and high throughput marker-assisted breeding using allele-specific SNP/Indel markers.
Suk-Man Kim,Jung-Pil Suh,Chung-Koon Lee,Yeong-Gyu Kim,Kshirod K. Jena 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07
Cold stress at the seedling stage is a major threat to rice production. Cold tolerance is controlled by complex genetic factors. We used an F7 recombinant inbred line (RIL) population of 123 individuals derived from the cross of a cold-tolerant japonica and a cold-sensitive indica cultivars, for QTL mapping. Phenotypic evaluation of the parents and RILs in an 18/8oC (day/night) cold-stress regime showed continuous variations for cold tolerance or sensitivity. Six QTLs for seedling cold tolerance were identified on chromosomes 1, 2, 4, 10, and 11 with percent phenotypic variation (R2) ranging from 6.1% to 16.5%. Three main-effect QTLs (qSCT1, qSCT4, and qSCT11) were detected in all cold-tolerant RILs which explained high sum of phenotypic variation (SPV) ranging from 27.1% to 50.6%. Two QTLs (qSCT1 and qSCT11) on chromosomes 1 and 11 were fine mapped. The marker In1-c3 from ORF LOC_Os01g69910 of the BAC clone B1455F06 encoding calmodulin-binding transcription activator (CAMTA) and another marker, In11-d1 from ORF LOC_Os11g37720 (Duf6 gene) of the BAC clone OSJNBa0029K08, co-segregated with seedling cold tolerance. These two InDel markers amplified 241-bp and 158-bp alleles, respectively, in cold-tolerant RILs, and in the cold-tolerant donor Jinbu, which were absent in cold-sensitive parent BR29 and cold-sensitive RILs.
Cytological Characterization of Interspecific Hybrids in Rice (Oryza sativa L.)
Eung Gi Jeong,Darshan S. Brar,Kyung Ho Kang,Heung Goo Hwang,Kshirod K. Jena,Ho Yeong Kim,Sang Nag Ahn,Gihwan Yi,Min Hee Nam 한국육종학회 2005 한국육종학회지 Vol.37 No.1
The wild species of Oryza are an important source of useful genes for resistance to biotic and abiotic stresses in rice. In this study, wide hybridization was used to widen the genepool of japonica rice cultivars. Interspecific crosses were made between three japonica rice cultivars and four wild species of the genus Oryza. Hybrids were produced normally through crosses between O. sativa (AA genome) and O. rufipogon (AA genome). However, hybrids between O. sativa and other distantly related wild species such as O. officinalis (CC genome), O. minuta (BBCC genome), and O. alta (CCDD genome) were produced following hybridization and embryo rescue. The hybrids were intermediate in their morphological characters, compared with the parents of cultivated and wild species. The hybrids between O. sativa and O. rufipogon were partially sterile but the hybrids between O. sativa and O. officinalis, O. sativa and O. minuta, O. sativa and O. alta were completely sterile. Cytological analysis of the interspecific hybrids, AA x CC, AA x BBCC, AA x CCDD showed irregular meiosis with predominant occurrence of univalents and unequal distribution of chromosomes at anaphase 1 of meiosis. Genomic In-situ Hybridization (GISH) analysis showed the presence of O. minuta chromosomes in the F₁ hybrids between O. sativa and O. minuta cross.