Fine mapping of a major quantitative trait loci, qSSP7, controlling the number of spikelets per panicle as a single Mendelian factor in rice

In our previous studies, one putative QTL affecting number of spikelets per panicle (SPP) was identified in the pericentromeric region of rice chromosome 7 using a recombinant inbred population. In order to define the QTL (qSPP7), RI50, a recombinant inbred line with 70% of genetic background same as the female parent of Zhenshan 97, was selected to produce near-isogenic lines for the target region in the present study. In a BC₂F₂ population consisting of 190 plants, the frequency distribution of SPP was shown to be discontinuous and followed the expected Mendelian ratios (1:2:1 by progeny test) for single locus segregation. qSPP7 was mapped to a 0.4 cM region between SSR marker RM3859 and RFLP marker C39 based on tests of the BC₂F₂ population and its progeny. Its additive and dominant effects on SPP were 51.1 and 24.9 spikelets, respectively. Of great interest, the QTL region also had effects on grain yield per plant (YD), 1,000 grain weight (GW), tillers per plant (TPP) and seed setting ratio (SR). Significant correlations were observed between SPP and YD (r = 0.66) and between SPP and SR (r = −0.29) in the progeny test. 1082 extremely small panicle plants of a BC₃F₂ population containing 8,400 individuals were further used to fine map the QTL. It turns out that qSPP7 co-segregated with two markers, RM5436 and RM5499 spanning a physical distance of 912.4 kb. Overall results suggested that recombination suppression occurred in the region and positional cloning strategy is infeasible for qSPP7 isolation. The higher grain yield of Minghui 63 homozygote as compared to the heterozygote suggested that Minghui 63 homozygote at qSPP7 in hybrid rice could further improve its yield. Y. Z. Xing and W. J. Tang contributed equally to this work.     

Additive and additive x additive interaction make important contributions to spikelets per panicle in rice near isogenic （Oryza sativa L.） lines

Epistasis plays an important role in the genetic basis of rice yield traits. Taking interactions into account in breeding programs will help the development of high-yielding rice varieties. In this study, three sets of near isogenic lines (NILs) targeting three QTLs for spikelets per panicle (SPP), namely qSPP1, qSPP2 and qSPP7, which share the same Zhenshan 97 genetic background, were used to produce an F₂ population in which the three QTLs segregated simultaneously. The genotypes of the individual F₂ plants at the three QTLs were replaced with three markers that are closely linked to the corresponding QTLs. These QTLs were validated in the F₂ and F₃ populations at the single marker level. qSPP7 exhibited major pleiotropic effects on SPP, plant height and heading date. Multifactor analysis of variance was performed for the F₂ population and its progeny. Additive (additive interaction between qSPP2 and qSPP7 had significant effects on SPP in both the F₂ population and its progeny. Both additive and additive (additive interactions could explain about 73% of the total SPP phenotypic variance. The SPP performance of 27 three-locus combinations was ranked and favorable combinations were recommended for rice breeding in different ecosystems.     

Additive and additive × additive interaction make important contributions to spikelets per panicle in rice near isogenic (Oryza sativa L.) lines

Epistasis plays an important role in the genetic basis of rice yield traits. Taking interactions into account in breeding programs will help the development of high-yielding rice varieties. In this study, three sets of near isogenic lines (NILs) targeting three QTLs for spikelets per panicle (SPP), namely qSPP1, qSPP2 and qSPP7, which share the same Zhenshan 97 genetic background, were used to produce an F 2 population in which the three QTLs segregated simultaneously. The genotypes of the individual F 2 plants at the three QTLs were replaced with three markers that are closely linked to the corresponding QTLs. These QTLs were validated in the F 2 and F 3 popula- tions at the single marker level. qSPP7 exhibited major pleiotropic effects on SPP, plant height and heading date. Multifactor analysis of variance was performed for the F 2 population and its progeny. Additive × additive interaction between qSPP2 and qSPP7 had significant effects on SPP in both the F 2 population and its progeny. Both additive and additive × additive interactions could explain about 73% of the total SPP phenotypic variance. The SPP performance of 27 three-locus combinations was ranked and favorable combinations were rec- ommended for rice breeding in different ecosystems.     

Quantitative trait loci for panicle size, heading date and plant height co-segregating in trait-performance derived near-isogenic lines of rice (Oryza sativa)

Near-isogenic lines (NILs) are ideal materials for precise estimation of quantitative trait loci (QTL) effects and map-based gene isolation. With the completion of the rice genome sequence, QTL isolation based on NILs is becoming a routine. In this study, a trait-performance derived NIL strategy was adopted to develop NILs. Two plants were identified within one inbred line of recombinant inbred lines (RILs, F₇ generation), exhibiting a significant difference in panicle size. By marker screening of the whole genome the genetic background of the two plants was estimated to be 98.7% identical. These two plants were selected as parents to produce a near-isogenic F₂ (NIL-F₂) population, consisting of 125 individuals, in which spikelets per panicle (SPP), grains per panicle (GPP), heading date (HD) and plant height (PH) were recorded. These four traits expressed discontinuous or bimodal distribution in the NIL-F₂ population and followed the expected segregation ratios for a single Mendelian factor by progeny tests. A partial dominant QTL for the four traits was mapped to the same interval flanked by RM310 and RM126 on chromosome 8. The QTL region explained 83.0, 80.2, 94.9 and 93.8% of trait variation of SPP, GPP, HD and PH in the progenies, respectively. Progeny tests also confirmed co-segregation of QTL for the four traits, tall plants consistently flowering late and carrying large panicles. Different NILs development strategies are discussed.     

Fine mapping SPP1, a QTL controlling the number of spikelets per panicle, to a BAC clone in rice (Oryza sativa)

Near isogenic lines (NILs) can be used to efficiently handle a target quantitative trait locus (QTL) by blocking genetic background noise. One QTL, SPP1, which controls the number of spikelets per panicle (SPP), was located on chromosome 1, near Gn1a, a cloned gene for rice production in a recombinant inbred line population. NILs of the SPP1 regions were quickly obtained by self-crossing recombinant inbred line 30 which is heterozygous around SPP1. Using a random NIL-F₂ population of 210 individuals, we mapped SPP1 to a 2.2-cM interval between RM1195 and RM490, which explained 51.1% of SPP variation. The difference in SPP between the two homozygotes was 44. F₂-1456, one NIL-F₂ plant, was heterozygous in the SPP1 region but was fixed in the region of Gn1a gene. This plant F₃ family showed a very wide variation in SPP, which suggested that it was SPP1 but Gn1a affected the variation of SPP in this population. In a word, SPP1 is a novel gene distinct from Gn1a. Four newly developed InDel markers were used for high-resolution mapping of SPP1 with a large NIL-F₂ population. Finally, it was narrowed down to a bacterial artificial chromosome clone spanning 107 kb; 17 open reading frames have been identified in the region. Of them, LOC_Os01g12160, which encodes an IAA synthetase, is the most interesting candidate gene.     

Validation of QTL for grain weight using MAS-derived pairs of NILs in bread wheat (Triticum aestivum L.)

Near isogenic lines (NILs) are ideal material for a variety of genetic studies including validation of specific QTL. In the present study, eight pairs of NILs for grain weight were developed, seven in the background of Raj3765, and one in the background of K9107. For this purpose, marker-assisted selection (MAS) was used for the transfer of three grain weight QTL (QGw.ccsu-1A.2, QGw.ccsu-1A.3 and QGw.ccsu-1B.1) that were earlier identified in our laboratory. Two genotypes of each of the eight pairs of NILs, differed for QTL alleles (QTL_Hgw derived from the donor parent and the QTL_Lgw derived from the recipient parent). Each pair of NILs involved a solitary QTL except one NIL, which differed for all the three QTL. The difference in thousand grain weight (TGW) in two NILs of an individual pair ranged from 2.8 to 7.5 g, thus validating the effect of the QTL for TGW, although the quantum of difference did not always match the phenotypic variance of the corresponding QTL. As expected, the NILs which involved all the three QTL had the maximum difference of 7.5 g in TGW, and the NILs which involved QTL, QGw.ccsu-1A.2 had minimum average difference of 2.8 g for TGW. The NILs produced during the present study may be used in future for MAS and for fine mapping of TGW QTL.

     

利用两种方法构建的近等基因系对水稻两个多效区段遗传效应进行评价

水稻每穗颖花数是水稻产量的重要构成因子之一。适当的抽穗期和株高对水稻高产是非常必要的。依据珍汕97和HR5衍生的重组自交系初步定位的结果, 利用高世代回交的方法构建了第7染色体同时控制抽穗期、株高和每穗颖花数的靶区段近等基因系(BC4F2); 利用基于重组自交系群体的杂合区段自交的方法构建了第8染色体同时控制抽穗期、株高和每穗颖花数的靶区段近等基因系, 并利用两个近等基因系对这两个多效区段的遗传效应进行了准确的评价。两个近等基因系的QTL分析结果表明, 3个性状都是由一个QTL或紧密连锁的QTL控制, 而且加性效应和显性效应的方向均相同; 同时3个性状在各自的近等基因系中呈现典型的双峰分布或不连续分布,这些结果暗示3个性状可能是一因多效的结果。文章还对抽穗期和株高与水稻产量的关系、3个性状显著正相关在育种中的应用及两种构建近等基因系方法的优缺点也进行了讨论。     

Molecular mapping of a novel gene, Grh5, conferring resistance to green rice leafhopper (Nephotettix cincticeps Uhler) in rice, Oryza sativa L.

The green rice leafhopper (GRH), Nephotettix cincticeps Uhler, is one of the most serious insect pests affecting cultivated rice (Oryza sativa L.) in temperate regions of East Asia. An accession of the wild rice species, Oryza rufipogon Griff. (W1962), was found to be highly resistant to GRH by an antibiosis test. To understand the genetic basis of the GRH resistance, a BC₁F₁ population derived from a cross between a susceptible Japonica variety, Taichung 65 (T65), and a highly resistant accession W1962 was analyzed by quantitative trait loci (QTL) mapping. A single major QTL for GRH resistance was detected on rice chromosome 8. A nearly isogenic population containing segments of the targeted QTL region derived from W1962 was then developed through advanced backcrossing with marker-assisted selection. Further molecular mapping using a BC₄F₂ population revealed that a new resistance gene, designated as Green rice leafhopper resistance 5 (Grh5), was located on the distal region of the long arm of chromosome 8 and tightly linked to the simple sequence repeat markers RM3754 and RM3761. A nearly isogenic line (NIL) carrying Grh5 was subsequently developed in the progeny of the mapping population. The resistance level of Grh5-NIL was compared with those of developed NILs for GRH resistance and was found to have the highest resistance. The DNA markers found to be closely linked to Grh5 would be useful for marker-assisted selection for the improvement of resistance to GRH in rice.     

A novel QTL <Emphasis Type="Italic">qSPP2.2</Emphasis> controlling spikelet per panicle identified from <Emphasis Type="Italic">Oryza longistaminata</Emphasis> (A. Chev. et Roehr.), mapped and transferred to <Emphasis Type="Italic">Oryza sativa</Emphasis> (L.)

Increasing the rice productivity from the current 10 to 12 tons/ha to meet the demand of estimated 8.8 billion people in 2035 is posing a major challenge. Wild relatives of rice contain some novel genes which can help in improving rice yield. Spikelet per panicle (SPP) is a valuable trait for determining yield potential in rice. In this study, a major QTL for increasing SPP has been identified, mapped, and transferred from African wild rice O. longistaminata to O. sativa (L.). The QTL was mapped on the long arm of chromosome 2 in a 167.1 kb region flanked by SSR markers RM13743 and RM13750, which are 1.0 cM apart, and is designated as qSPP2.2. The QTL explained up to 30% of phenotypic variance in different generations/seasons and showed positive additive effect of allele contributed by O. longistaminata. In addition, O. longistaminata allele in qSPP2.2 contributed to increase in grains per panicle, but decrease in the tillers per plant. The 167.1 kb region contains 23 predicted genes. Based on the functional annotation, three genes, LOC_Os02g44860, LOC_Os02g44990, and LOC_Os02g45010, were selected as putative candidates for characterization. Sequence analysis of the three genes revealed functional variations between the parental lines for LOC_Os02g44990 and a variation in 5′UTR for LOC_Os02g45010 which will help further to identify putative candidate gene(s). This is the first yield component QTL to be identified, mapped, and transferred from O. longistaminata.     

High‐density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe

Miscanthus is a perennial C₄ grass that has recently become an important bioenergy crop. The efficiency of breeding improved Miscanthus biomass cultivars could be greatly increased by marker‐assisted selection. Thus, a high‐density genetic map is critical to Miscanthus improvement. In this study, a mapping population of 261 F₁ progeny was developed from a cross between two diploid M. sinensis cultivars, ‘Strictus’ and ‘Kaskade’. High‐density genetic maps for the two parents were produced with 3044 newly developed single nucleotide polymorphisms (SNPs) obtained from restriction site‐associated DNA sequencing, and 138 previously mapped GoldenGate SNPs. The female parent (‘Strictus’) map spanned 1599 cM, with 1989 SNPs on 19 linkage groups, and an average intermarker spacing of 0.8 cM. The length of the male parent (‘Kaskade’) map was 1612 cM, with 1821 SNPs, and an average intermarker spacing of 0.9 cM. The utility of the map was confirmed by locating quantitative trait loci (QTL) for the zebra‐striped trait, which was segregating in this population. Three QTL for zebra‐striped presence/absence (zb1, zb2 on LG 7, and zb3 on LG 10) and three for zebra‐striped intensity (zbi1, zbi2, zbi3 on LGs 7, 10, 3) were identified. Each allele that caused striping was recessive. Incomplete penetrance was observed for each zb QTL, but penetrance was greatest when two or more zb QTL were homozygous for the causative alleles. Similarly, the intensity of striping was greatest when two or more zbi QTL were homozygous for alleles that conferred the trait. Comparative mapping indicated putative correspondence between zb3 and/or zbi2 on LG 10 to previously sequenced genes conferring zebra stripe in maize and rice. These results demonstrate that the new map is useful for identifying marker–trait associations. The mapped markers will become a valuable community resource, facilitating comparisons among studies and the breeding of Miscanthus.     

GENETIC MAPPING OF THE LAMINARIA JAPONICA (LAMINARALES,PHAEOPHYTA) USING AMPLIFIED FRAGMENT LENGTH POLYMORPHISM MARKERS1

To establish a molecular‐marker‐assisted system of breeding and genetic study for Laminaria japonica Aresch., amplified fragment length polymorphism (AFLP) was used to construct a genetic linkage map of L. japonica featuring 230 progeny of F₂ cross population. Eighteen primer combinations produced 370 polymorphic loci and 215 polymorphic loci segregated in a 3:1 Mendelian segregation ratio (P ≤ 0.05). Of the 215 segregated loci, 142 were ordered into 27 linkage groups. The length of the linkage groups ranged from 6.7 to 90.3 centimorgans (cM) with an average length of 49.6 cM, and the total length was 1,085.8 cM, which covered 68.4% of the estimated 1,586.9 cM genome. The number of mapped markers on each linkage group ranged from 2 to 12, averaging 5.3 markers per group. The average density of the markers was 1 per 9.4 cM. Based on the marker density and the resolution of the map, the constructed linkage map can satisfy the need for quantitative trait locus (QTL) location and molecular‐marker‐assisted breeding for Laminaria.     

Characterization of <Emphasis Type="Italic">fs10.1</Emphasis>, a major QTL controlling fruit elongation in <Emphasis Type="Italic">Capsicum</Emphasis>

We previously identified fs10.1 as a major QTL controlling fruit shape (index of length to width) in an interspecific F₂ cross of Capsicum annuum (round fruit) × C. chinense (elongated fruit) in pepper. To more precisely map and characterize the QTL, we constructed near-isogenic lines for fs10.1 and mapped it in a BC₄F₂ population. In this population, fs10.1 segregated as a Mendelian locus and mapped 0.3 cM away from the closest molecular marker. We further verified the effect of fs10.1 in an F₂ population from an independent cross between elongated- and conical-fruited parents. To identify additional allelic variation at fruit shape loci, we screened an EMS-mutagenized population of the blocky-fruited cv. Maor and identified the mutant E-1654 with elongated fruit. This fruit shape mutation was mapped to the fs10.1 region and was determined to be allelic to the QTL. By measuring fruit shape of near-isogenic lines for fs10.1 during fruit development, we found that the shape of the fruit is determined primarily in the first 2 weeks after anthesis. Histological measurements of cell size and cell shape in pericarp sections of fruits of the isogenic lines throughout fruit development indicated that the shape of the fruit is determined primarily by cell shape and that the development of fruit shape is correlated with cell shape.     

A quantitative trait locus for reduced culm internode length in barley segregates as a Mendelian gene

Yield losses caused by lodging in cereals can be partially controlled by reducing plant height. A progeny of recombinant inbred lines from a cross of two Japanese barley varieties was used to study the inheritance of culm and culm internode lengths. An unexpected QTL for reduced culm length (qCUL), which affected mainly the length of the third and fourth culm internodes, was contributed by ‘Kanto Nakate Gold’. This QTL was also associated with reduced lodging in two experiments. A near-isogenic line (culm length 62.9–73.4 cm) in an ‘Azumamugi’ background, carrying a chromosome segment containing the qCUL allele from Kanto Nakate Gold, was significantly shorter than its recurrent parent (82.9–89.4 cm). The F₂ generation from the next backcross segregated for plant height in a Mendelian monogenic ratio. The qCUL locus was shown to be tightly linked (1.2 cM) with the codominant STS marker ABG608. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in <Emphasis Type="Italic">Lolium perenne</Emphasis>

A mapping population was created to detect quantitative trait loci (QTL) for resistance to stem rust caused by Puccinia graminis subsp. graminicola in Lolium perenne. A susceptible and a resistant plant were crossed to produce a pseudo-testcross population of 193 F₁ individuals. Markers were produced by the restriction-site associated DNA (RAD) process, which uses massively parallel and multiplexed sequencing of reduced-representation libraries. Additional simple sequence repeat (SSR) and sequence-tagged site (STS) markers were combined with the RAD markers to produce maps for the female (738 cM) and male (721 cM) parents. Stem rust phenotypes (number of pustules per plant) were determined in replicated greenhouse trials by inoculation with a field-collected, genetically heterogeneous population of urediniospores. The F₁ progeny displayed continuous distribution of phenotypes and transgressive segregation. We detected three resistance QTL. The most prominent QTL (qLpPg1) is located near 41 cM on linkage group (LG) 7 with a 2-LOD interval of 8 cM, and accounts for 30–38% of the stem rust phenotypic variance. QTL were detected also on LG1 (qLpPg2) and LG6 (qLpPg3), each accounting for approximately 10% of phenotypic variance. Alleles of loci closely linked to these QTL originated from the resistant parent for qLpPg1 and from both parents for qLpPg2 and qLpPg3. Observed quantitative nature of the resistance may be due to partial-resistance effects against all pathogen genotypes, or qualitative effects completely preventing infection by only some genotypes in the genetically mixed inoculum. RAD markers facilitated rapid construction of new genetic maps in this outcrossing species and will enable development of sequence-based markers linked to stem rust resistance in L. perenne.     

Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factors

 Fine mapping was carried out on three putative QTLs (tentatively designated as Hd-1 to Hd-3) of five such QTLs controlling heading date in rice that had been earlier identified using an F₂ population derived from a cross between a japonica variety, ‘Nipponbare’, and an indica variety, ‘Kasalath’, using progeny backcrossed with ‘Nipponbare’ as the recurrent parent. One BC₃F₂ and two BC₃F₁ plants, in which the target QTL regions were heterozygous and most other chromosomal regions were homozygous for the ‘Nipponbare’ allele, were selected as the experimental material. Self-pollinated progeny (BC₃F₂ and BC₃F₃) of the BC₃F₁ or BC₃F₂ showed continuous variation in days to heading. By means of progeny testing based on BC₃F₃ or BC₃F₄ lines, we determined the genotypes of each BC₃F₂ or BC₃F₃ individual at target QTLs. Their segregation patterns fitted Mendelian inheritance ratios. When the results obtained by RFLP analysis and progeny tests were combined, Hd-1, Hd-2 and Hd-3 were mapped precisely on chromosomes 6, 7 and 6, respectively, of a rice RFLP linkage map. The results demonstrated that QTLs can be treated as Mendelian factors. Moreover, these precise locations were in good agreement with the regions estimated by QTL analysis of the initial F₂ population, demonstrating the high reliability of QTL mapping using a high-density linkage map. Received: 5 November 1997 / Accepted: 10 February 1998     

High-resolution mapping of <Emphasis Type="Italic">Rsn1</Emphasis>, a locus controlling sensitivity of rice to a necrosis-inducing phytotoxin from <Emphasis Type="Italic">Rhizoctonia solani</Emphasis> AG1-IA

Rhizoctonia solani is a necrotrophic fungal pathogen that causes disease on many crop-plant species. Anastomosis group 1-IA is the causal agent of sheath blight of rice (Oryza sativa L.), one of the most important rice diseases worldwide. R. solani AG1-IA produces a necrosis-inducing phytotoxin and rice cultivar’s sensitivity to the toxin correlates with disease susceptibility. Unlike genetic analyses of sheath blight resistance where resistance loci have been reported as quantitative trait loci, phytotoxin sensitivity is inherited as a Mendelian trait that permits high-resolution mapping of the sensitivity genes. An F₂ mapping population derived from parent cultivars ‘Cypress’ (toxin sensitive) and ‘Jasmine 85’ (toxin insensitive) was used to map Rsn1, the necrosis-inducing locus. Initial mapping based on 176 F₂ progeny and 69 simple sequence repeat (SSR) markers located Rsn1 on the long arm of chromosome 7, with tight linkage to SSR marker RM418. A high-resolution genetic map of the region was subsequently developed using a total of 1,043 F₂ progeny, and Rsn1 was mapped to a 0.7 cM interval flanked by markers NM590 and RM418. Analysis of the corresponding 29 Kb genomic sequences from reference cultivars ‘Nipponbare’ and ‘93-11’ revealed the presence of four putative genes within the interval. Two are expressed cytokinin-O-glucosyltransferases, which fit an apoptotic pathway model of toxin activity, and are individually being investigated further as potential candidates for Rsn1.     

Molecular mapping for resistance to pea rust caused by <Emphasis Type="Italic">Uromyces fabae</Emphasis> (Pers.) de-Bary

Pea rust caused by Uromyces fabae (Pers.) de-Bary is a major problem in warm humid regions causing huge economic losses. A mapping population of 136 F_6:7 recombinant inbred lines (RILs) derived from the cross between pea genotypes, HUVP 1 (susceptible) and FC 1 (resistant) was evaluated in polyhouse as well as under field conditions during two consecutive years. Infection frequency (IF) and area under disease progress curve (AUDPC) were used for evaluation of rust reaction of the RILs. A linkage map was constructed with 57 polymorphic loci selected from 148 simple sequence repeats (SSRs), 3 sequence tagged sites (STS), and 2 random amplified polymorphic (RAPD) markers covering 634 cM of genetic distance on the seven linkage groups of pea with an average interval length of 11.3 cM. Composite interval mapping (CIM) revealed one major (Qruf) and one minor (Qruf1) QTL for rust resistance on LGVII. The LOD (5.2–15.8) peak for Qruf was flanked by SSR markers, AA505 and AA446 (10.8 cM), explaining 22.2–42.4% and 23.5–58.8% of the total phenotypic variation for IF and AUDPC, respectively. The minor QTL was environment-specific, and it was detected only in the polyhouse (LOD values 4.2 and 4.8). It was flanked by SSR markers, AD146 and AA416 (7.3 cM), and explained 11.2–12.4% of the total phenotypic variation. The major QTL Qruf was consistently identified across all the four environments. Therefore, the SSR markers flanking Qruf would be useful for marker-assisted selection for pea rust (U. fabae) resistance.     

AFLP and PCR-based markers linked to Rf3, a fertility restorer gene for S cytoplasmic male sterility in maize

The Rf3 gene restores the pollen fertility disturbed by S male sterile cytoplasm. In order to develop molecular markers tightly linked to Rf3, we used amplified fragment length polymorphism (AFLP) technique with near isogenic lines (NILs) and bulk segregant analysis (BSA). A BC₁F₁ population from a pair of NILs with different Rf3 locus was constructed and 528 primer combinations was screened. A linkage map was constructed around the Rf3 locus, which was mapped on the distal region of chromosome 2 long arm with the help of SSR marker UMC2184. The closest marker E7P6 was 0.9 cM away from Rf3. Marker E3P1, 2.4 cM from Rf3, and E12M7, 1.8 cM from Rf3, were converted into a codominant CAPS and a dominant SCAR marker, and designated as CAPSE3P1 and SCARE12M7, respectively. These markers are useful for marker-assisted selection and map-based cloning of the Rf3 gene.     

RFLP tagging of a gene for aroma in rice

Summary We report here the identification of a DNA marker closely linked to a gene for aroma in rice. The DNA marker was identified by testing 126 mapped rice genomic, cDNA, and oat cDNA, clones as hybridization probes against Southern blots, consisting of DNA from a pair of nearly isogenic lines (NILs) with or without the aroma gene. Chromosomal segments introgressed from the donor genome were distinguished by RFLPs between the NILs. Linkage association of the clone with the gene was verified using an F₃ segregating for aroma. Cosegregation of the scented phenotype and donor-derived allele indicated the presence of linkage between the DNA marker and the gene. RFLP analysis showed that the gene is linked to a single-copy DNA clone, RG28, on chromosome 8, at a distance of 4.5 cM. The availability of a linked DNA marker may facilitate early selection for the aroma gene in rice breeding programs.     

QTL analysis and mapping of pi21, a recessive gene for field resistance to rice blast in Japanese upland rice

Field resistance is defined as the resistance that allows effective control of a parasite under natural field conditions and is durable when exposed to new races of that parasite. To identify the genes for field resistance to rice blast, quantitative trait loci (QTLs) conferring field resistance to rice blast in Japanese upland rice were detected and mapped using RFLP and SSR markers. QTL analysis was carried out in F₄ progeny lines from the cross between Nipponbare (moderately susceptible, lowland) and Owarihatamochi (resistant, upland). Two QTLs were detected on chromosome 4 and one QTL was detected on each of chromosomes 9 and 12. The phenotypic variation explained by each QTL ranged from 7.9 to 45.7% and the four QTLs explained 66.3% of the total phenotypic variation. Backcrossed progeny lines were developed to transfer the QTL with largest effect using the susceptible cultivar Aichiasahi as a recurrent parent. Among 82 F₃ lines derived from the backcross, resistance segregated in the expected ratio of resistant 1 : heterozygous 2 : susceptible 1. The average score for blast resistance measured in the field was 4.2 ± 0.67, 7.5 ± 0.51and 8.2 ± 0.66, for resistant, heterozygous and susceptible groups, respectively. The resistance gene, designated pi21, was mapped on chromosome 4 as a single recessive gene between RFLP marker loci G271 and G317 at a distance of 5.0 cM and 8.5 cM, respectively. The relationship to previously reported major genes and QTLs conferring resistance to blasts, and the significance of marker-assisted selection to improve field resistance, are discussed. Received: 8 June 2000 / Accepted: 24 November 2000