Molecular Linkage Map Research Articles

Sequence tagged site markers linked to the sbm1 gene for resistance to pea seedborne mosaic virus in pea

AbstractResistance to pea seed‐borne mosaic virus (PSbMV) pathotype P‐1 in peas is conferred by sbm1 with recessive inheritance. PSbMV is an economically important pathogen with world‐wide distribution that causes significant losses in pea yield and reduces seed and produce quality. The sbm1 gene was previously mapped to linkage group VI on molecular linkage maps of the pea genome. To improve plant breeders’ ability to develop varieties resistant to PSbMV, two random amplified polymorphic DNA markers (G05_2537 and L01_910) and one restriction fragment length polymorphism (P446) linked to sbm1 have been identified. The genomic sequences for these markers have been characterized and the information used to develop three simple polymerase chain reaction‐based STS (sequence tagged site) assays. Linkage analysis in two F2 populations showed that the most tightly linked of these three STS loci (sG05_2537) is approximately 4 cM from sbm1. Characterization of a collection of resistant and susceptible germplasm demonstrated a strong correlation between STS alleles and sbm1 alleles, indicating the utility of these markers for marker‐assisted selection in breeding programmes using a range of germplasm sources.

Molecular linkage map of allotetraploid cotton ( Gossypium hirsutum L. x Gossypium barbadense L.) with a haploid population.

In the present study, a haploid population from the cross of the two cultivated allotetraploid cottons, Gossypium hirsutum L. and Gossypium barbadense L., was developed by means of Vsg, a virescently marked semigamous line of Sea island cotton, and some target haploids were successfully doubled with colchicine. A molecular linkage map was constructed with 58 doubled and haploid plants. Among the total of 624 marker loci (510 SSRs and 114 RAPDs), 489 loci were assembled into 43 linkage groups and covered 3,314.5 centi-Morgans (cM). Using the monosomic and telodisomic genetic stocks, the linkage groups of the present map were associated with chromosomes of the allotetraploid genome, and some of the unassociated groups were connected to corresponding A or D subgenomes. Through the analysis of the assignment of the duplicated SSR loci in the chromosomes or the linkage groups, ten pairs of possible homoeologous chromosome (or linkage group) regions were identified. Among them, the pairs of Chrs. 1 and 15, Chrs. 4 and 22, and Chrs. 10 and 20 had already been determined as homoeologous by classical genetic and cytogenetic research, and the pair of Chrs. 9 and 23 had also been identified by the ISH method of molecular cytogenetics. But, from present research, it was assumed that Chrs. 5 and 18 might be a new pair of homoeologous chromosomes of the allotetraploid cotton genome detected by molecular mapping of the cotton genome.

Genetic analysis of floral anthocyanin pigmentation traits in Asiatic hybrid lily using molecular linkage maps.

To understand the genetic background of two floral anthocyanin pigmentation traits, anthocyanin pigmentation in the flower tepals and spot formation, in the Asiatic hybrid lily (2n = 24), segregation of the two traits among 96 F(1) plants derived from a cross between commercial cultivars 'Montreux' and 'Connecticut King' were investigated. 'Montreux' has anthocyanin pigmentation in the tepals with many spots, and 'Connecticut King' has flowers with carotenoid pigmentation without spots. The F(1) plants with or without anthocyanin pigment in the tepals segregated with a 1:1 segregation ratio, indicating that a single gene controls anthocyanin pigmentation in the tepals. The number of spots per square centimeter of all tepals showed continuous distribution in the F(1) plants. To map the loci for the two anthocyanin pigmentation traits, molecular linkage maps in the Asiatic hybrid lily were constructed using a double pseudo-testcross strategy, with the same F(1) plants used for phenotypic evaluation, and 212 PCR-based DNA markers. The trait for anthocyanin pigmentation in tepals was used as a trait marker. The map of 'Montreux' comprised 95 markers in 26 linkage groups, and the map of 'Connecticut King' used 119 markers in 24 linkage groups. The total map lengths were 867.5 and 1,114.8 cM, respectively. The trait locus for anthocyanin pigmentation in the tepals was between markers ASR35-180 and P506-40 in linkage group 1 of the 'Montreux' map with a map distance of 1.2 cM and 2.6 cM, respectively. A single-point analysis of quantitative trait loci (QTLs) for tepal spot number identified two putative QTLs in linkage groups 1 and 19 of the 'Connecticut King' map. One putative QTL in linkage group 19 explained 64% of the total phenotypic variation. Because both putative QTLs were mapped on the linkage map of 'Connecticut King' that has no spots, dominant alleles of them might suppress spot formation.

Molecular linkage map of Einkorn wheat: mapping of storage-protein and soft-glume genes and bread-making quality QTLs.

Two molecular maps of Triticum monococcum L were produced and integrated. The integrated map includes a total of 477 markers, 32 RFLPs, 438 AFLPs, one morphological (soft glume (Sog)) and six storage-protein markers, and covers 856 cM. The trait Sog with the recessive allele sog maps to linkage group 2S. Probably, this is the T. monococcum homologue of Tg and Tg2 in hexaploid and tetraploid wheats, respectively. Loci coding for seed storage proteins were allocated to chromosomes 1L (HMW GLU1,2 and Glu1), 1S (LMW GLU6,7, LMW GLU1-4, omega GLI1-4, gamma GLI5 and Gli-1) and 6L (alpha/beta GLI7-14). Parameters related to bread-making quality (SDS sedimentation volume, specific sedimentation volume (SSV) and total protein content) were studied in one of the two populations. A QTL that is consistently present across environments was detected for SDS sedimentation volume and for SSV. The position of the QTL on chromosome 1S was in close agreement with the map positions of storage-protein loci. A second QTL was mapped on chromosome 5. For protein content, two significant QTLs were mapped to linkage groups 1 and 5.

An update of the Courtot x Chinese Spring intervarietal molecular marker linkage map for the QTL detection of agronomic traits in wheat.

We made an update of the intervarietal molecular marker linkage map of the wheat genome developed using a doubled-haploid (DH) population derived from the cross between the cultivars "Courtot" and "Chinese Spring". This map was constructed using 187 DH lines and 659 markers. The genome was well covered (more than 95%) except for chromosomes from homoeologous group 4 and chromosomes 5D and 7D, which had gaps slightly larger than 50 cM. A core-map based on a set of 200 anchor loci (one marker each 18.4 cM) was developed. The total length of this map was 3,685 cM which is similar to the size of the international reference map of the ITMI population (3,551 cM). Map coverage was identical for the three genomes (A, B and D) and for the number of anchor loci, as well as for the size of the map. Using this map, QTLs for several agronomic traits were detected on phenotypic data from the population grown in Clermont-Ferrand (France) under natural field conditions over 6 years, and in Norwich (UK) in controlled conditions and under natural field conditions in 1 year. Almost all of the 21 chromosomes were involved in at least one trait. However, several regions seemed to contain gene clusters either for grain traits (and thus bread-making quality) or plant development traits.

Genetic Linkage in Soybean

Mapping mutants of classical linkage groups 6 and 8 (CLGs 6 and 8) in soybean [Glycine max (L.) Merr.] can enhance the identification of important agronomic traits. Genetic data suggest that CLGs 6 and 8 may belong to the same linkage group. Our objectives were to determine if CLGs 6 and 8 are the same or different linkage groups and to determine the gene order. Genotypes containing mutants of CLGs 6 and 8 and mutants of other CLGs were crossed in various combinations. Data for the different characters were collected from F 2 populations and F 2:3 families. Recombination values confirmed that CLG 6 characters, Df2 and Y 11 were linked (R = 27.0 ± 5.9), Df 2 was linked to Ms 1 (CLG 8) (R = 24.8 ± 1.2) and to W 1 (CLG 8) (R = 36.4 ± 13), and Y 11 was linked to Ms 1 (R = 31.7 ± 1.4). F 2 data suggested that Y 11 segregated independently of W 1 , while F 2:3 data indicated the two were linked (R = 38.4 ± 3.2). Our data indicated that CLGs 6 and 8 belong to the same linkage group, which is molecular linkage group F (MLG F), and chromosome 13. Y 11 and Adh 1 are at the ends of the chromosome segment studied, and Y 23 is located between Ms 6 and St 5 . Recombination values among the other loci of CLG 8, and between them and loci of other CLGs were consistent with published values. This information will be useful in the reassignment of CLGs, ordering of loci, and will enhance molecular genetic linkage mapping in soybean.

Simple sequence repeat map of the sunflower genome.

Several independent molecular genetic linkage maps of varying density and completeness have been constructed for cultivated sunflower ( Helianthus annuus L.). Because of the dearth of sequence and probe-specific DNA markers in the public domain, the various genetic maps of sunflower have not been integrated and a single reference map has not emerged. Moreover, comparisons between maps have been confounded by multiple linkage group nomenclatures and the lack of common DNA markers. The goal of the present research was to construct a dense molecular genetic linkage map for sunflower using simple sequence repeat (SSR) markers. First, 879 SSR markers were developed by identifying 1,093 unique SSR sequences in the DNA sequences of 2,033 clones isolated from genomic DNA libraries enriched for (AC)(n) or (AG)(n) and screening 1,000 SSR primer pairs; 579 of the newly developed SSR markers (65.9% of the total) were polymorphic among four elite inbred lines (RHA280, RHA801, PHA and PHB). The genetic map was constructed using 94 RHA280 x RHA801 F(7) recombinant inbred lines (RILs) and 408 polymorphic SSR markers (462 SSR marker loci segregated in the mapping population). Of the latter, 459 coalesced into 17 linkage groups presumably corresponding to the 17 chromosomes in the haploid sunflower genome ( x = 17). The map was 1,368.3-cM long and had a mean density of 3.1 cM per locus. The SSR markers described herein supply a critical mass of DNA markers for constructing genetic maps of sunflower and create the basis for unifying and cross-referencing the multitude of genetic maps developed for wild and cultivated sunflowers.

A comparative genetic linkage map of eggplant (Solanum melongena) and its implications for genome evolution in the solanaceae.

A molecular genetic linkage map based on tomato cDNA, genomic DNA, and EST markers was constructed for eggplant, Solanum melongena. The map consists of 12 linkage groups, spans 1480 cM, and contains 233 markers. Comparison of the eggplant and tomato maps revealed conservation of large tracts of colinear markers, a common feature of genome evolution in the Solanaceae and other plant families. Overall, eggplant and tomato were differentiated by 28 rearrangements, which could be explained by 23 paracentric inversions and five translocations during evolution from the species' last common ancestor. No pericentric inversions were detected. Thus, it appears that paracentric inversion has been the primary mechanism for chromosome evolution in the Solanaceae. Comparison of relative distributions of the types of rearrangements that distinguish pairs of solanaceous species also indicates that the frequency of different chromosomal structural changes was not constant over evolutionary time. On the basis of the number of chromosomal disruptions and an approximate divergence time for Solanum, approximately 0.19 rearrangements per chromosome per million years occurred during the evolution of eggplant and tomato from their last ancestor. This result suggests that genomes in Solanaceae, or at least in Solanum, are evolving at a moderate pace compared to other plant species.

Molecular and physical mapping of genes affecting awning in wheat

AbstractQuantitative trait loci (QTL) for three traits related to awning (awn length at the base, the middle and the top of the ear) in wheat were mapped in a doubled‐haploid line (DH) population derived from the cross between the cultivars ‘Courtot’ (awned) and ‘Chinese Spring’ (awnless) and grown in Clermont‐Ferrand, France, under natural field conditions. A molecular marker linkage map of this cross that was previously constructed based on 187 DH lines and 550 markers was used for the QTL mapping. The genome was well covered (more than 95%) and a set of anchor loci regularly spaced (one marker every 20.8 cM) was chosen for marker regression analysis. For each trait, only two consistent QTL were identified with individual effects ranging from 8.5 to 45.9% of the total phenotypic variation. These two QTL cosegregated with the genes Hd on chromosome 4A and B2 on chromosome 6B, which are known to inhibit awning. The results were confirmed using ‘Chinese Spring’ deletion lines of these two chromosomes, which have awned spikes, while ‘Chinese Spring’ is usually awnless. No quantitative trait locus was detected on chromosome 5A where the B1 awn‐inhibitor gene is located, suggesting that both ‘Courtot’ and ‘Chinese Spring’ have the same allelic constitution at this locus. The occurrence of awned speltoid spikes on the deletion lines of this chromosome suggests that ‘Chinese Spring’ and ‘Courtot’ have the dominant B1 allele, indicating that B1 alone has insufficient effect to induce complete awn inhibition.

Identification of RAPD Markers Linked to Five Marker Genes (blu, dgs, y, arg, and a Flat Pod Mutant) in Common Bean

The development of a complete linkage map, including both classical (visible) and molecular markers, is important to understand the genetic relationships among different traits in common bean (Phaseolus vulgaris L.). The objective of this study was to integrate classical marker genes into previously constructed molecular linkage maps in common bean. Bulked segregant analysis was used to identify 10 random amplified polymorphic DNA (RAPD) markers linked to genes for five classical marker traits: dark green savoy leaf (dgs), blue flower (blu), silvery [Latin: argentum] green pod (arg), yellow wax pod (y) and flat pod (a spontaneous mutation from round to flat pod in `Hialeah' snap bean). The genes for dark green savoy leaf (dgs) and blue flower (blu) were located in a previously constructed molecular linkage map. These results indicate that classical marker genes and molecular markers can be integrated to form a more complete and informative genetic linkage map. Most of the RAPD markers were not polymorphic in the two mapping populations used, and molecular markers from those mapping populations were not polymorphic in the F2 populations used to develop the RAPD markers. Alternative genetic hypotheses for the pod shape mutation in `Hialeah' are discussed, and the experimental difficulties of pod shape classification are described.

DIFFERENTIAL RESPONSE OF RICE PLANTS TO LOW-PHOSPHORUS STRESS AND ITS PHYSIOLOGICAL ADAPTIVE MECHANISM

ABSTRACT Two rice genotypes, JX17 (Oryza sativa ssp. japonica) and ZYQ8 (Oryza sativa ssp. indica), which had been the parents of the 127-line double haploid (DH) population for construction of molecular linkage map, were chosen to study their response to low phosphorus (P) stress. The results indicated that JX17 had advantages over ZYQ8 on some traits associated with phosphorus uptake efficiency, such as root dry weight, root-exuded acid phosphatase activity, root-exuded organic acids and proton. Consequently, JX17 had higher relative total dry weight and was regarded as the non-sensitive genotype to low phosphorus stress. Physiological response of the two genotypes to P deficiency was studied in monoculture and in mixed culture. The results showed that, compared with monoculture, JX17 absorbed more P and had higher biomass in mixed culture condition under P stress. ZYQ8, by contrast, suffered from P stress to a much greater extent, with lower P uptake and biomass. JX17 had a higher P uptake rate expressed as P amount per root length which is suggested to be the main reason for its insensitivity to low P stress.

Isolation and linkage mapping of disease‐resistance‐like sequences from various rice cultivars, containing different recognition specificities

AbstractDegenerated oligonucleotide primers identified from the nucleotide‐binding sites of known disease resistance (R) genes were used from rice cultivars harbouring different recognition specificities to amplify and clone homologous sequences of R genes. A total of 68 non‐redundant clones, which showed various degrees of sequence homology to R genes, were obtained from 18 rice cultivars. These clones had a high degree of sequence diversity both in the nucleotides and in the predicted amino acids, and were classified into five groups using clustal analysis. Fifteen of the 68 clones were mapped to 17 loci on chromosomes 3, 5, 11 and 12 in the rice molecular linkage map. The loci of the mapped clones correlated with the locations of known rice R genes for blast resistance and bacterial blight resistance on chromosomes 11 and 12. Other mapped loci occurred in cluster on chromosome 3, and correlated with the position of a quantitative trait locus for bacterial blight resistance. The mapping of the R gene homologues may aid the identification and isolation of R gene candidates.

Molecular mapping of the intermedium spike-c ( int-c) and non-brittle rachis 1 ( btr1) loci in barley ( Hordeum vulgare L.).

Lateral spikelet fertility and a non-brittle rachis are key characters in studying the evolution of barley. The fertility of lateral spikelets is controlled predominantly by the alleles at the vrs1 locus on chromosome 2HL and is modified by the alleles at the int-c locus on chromosome 4HS. The non-brittle rachis is controlled by alleles at two tightly linked loci, btr1 and btr2, on chromosome 3HS. This paper presents the integration of the int-c and btr1 loci in molecular linkage maps of barley. The int-c locus was mapped to the end of chromosome 4HS, 8.2 cM distal from the MWG2033 locus. The analysis was followed by a composite interval mapping of quantitative trait loci, which verified the position of the int-c locus. Linkage analysis using recombinant inbred lines showed that the btr1 locus is flanked between two AFLP loci, e14m27.4.1 and e15m19.7, with map distances of 3.1 cM and 4.2 cM, respectively. The molecular markers will expedite further high-density mapping of the int-c and btr1 loci.

Genomic organization of glycinin genes in soybean.

Glycinin is the predominant seed storage protein in most soybean varieties. Previously, five major genes (designated Gy1 to Gy5) encoding glycinin subunits have been described. In this report two new genes are identified and mapped: a glycinin pseudogene, gy6, and a functional gene, Gy7. Messenger RNA for the gy6 pseudogene is not detected in developing seeds. While Gy7 mRNA was present at the midmaturation stage of seed development in the soybean variety Resnik, the steady state amount of this message was at least an order of magnitude less-prevalent than the mRNA encoding each of the other five glycinin subunits. Even though the amino-acid sequence of the glycinin subunit G7 is related to the other five soybean 11S subunits, it does not fit into either the Group-1 (G1, G2, G3) or the Group-2 (G4, G5) glycinin subunit families. The Gy7 gene is tandemly linked 3' to Gy3 on Linkage Group L (chromosome 19) of the public molecular linkage map. By contrast, the gy6 gene occupies a locus downstream from Gy2 on Linkage Group N (chromosome 3) in a region that is related to the position where Gy7 is located on chromosome 19.

A molecular linkage map of tomato displaying chromosomal locations of resistance gene analogs based on a Lycopersicon esculentum x Lycopersicon hirsutum cross.

A molecular linkage map of tomato was constructed based on a BC1 population (N = 145) of a cross between Lycopersicon esculentum Mill. line NC84173 (maternal and recurrent parent) and Lycopersicon hirsutum Humb. and Bonpl. accession PI126445. NC84173 is an advanced breeding line that is resistant to several tomato diseases, not including early blight (EB) and late blight (LB). PI126445 is a self-incompatible accession that is resistant to many tomato diseases, including EB and LB. The map included 142 restriction fragment length polymorphism (RFLP) markers and 29 resistance gene analogs (RGAs). RGA loci were identified by PCR amplification of genomic DNA from the BC1 population, using ten pairs of degenerate oligonucleotide primers designed based on conserved leucine-rich repeat (LRR), nucleotide binding site (NBS), and serine (threonine) protein kinase (PtoKin) domains of known resistance genes (R genes). The PCR-amplified DNAs were separated by denaturing polyacrylamide gel electrophoresis (PAGE), which allowed separation of heterogeneous products and identification and mapping of individual RGA loci. The map spanned 1469 cM of the 12 tomato chromosomes with an average marker distance of 8.6 cM. The RGA loci were mapped to 9 of the 12 tomato chromosomes. Locations of some RGAs coincided with locations of several known tomato R genes or quantitative resistance loci (QRLs), including Cf-1, Cf-4, Cf-9, Cf-ECP2, rx-1, and Cm1.1 (chromosome 1); Tm-1 (chromosome 2); Asc (chrromosme 3); Pto, Fen, and Prf (chromosome 5); 01-1, Mi, Ty-1, Cm6.1, Cf-2, CF-5, Bw-5, and Bw-1 (chromosome 6); I-1, 1-3, and Ph-1 (chromosome 7); Tm-2a and Fr1 (chromosome 9); and Lv (chromosome 12). These co-localizations indicate that the RGA loci were either linked to or part of the known R genes. Furthermore, similar to that for many R gene families, several RGA loci were found in clusters, suggesting their potential evolutionary relationship with R genes. Comparisons of the present map with other molecular linkage maps of tomato, including the high density L. esculentum x Lycopersicon pennellii map, indicated that the lengths of the maps and linear order of RFLP markers were in good agreement, though certain chromosomal regions were less consistent than others in terms of the frequency of recombination. The present map provides a basis for identification and mapping of genes and QTLs for disease resistance and other desirable traits in PI126445 and other L. hirsutum accessions, and will be useful for marker-assisted selection and map-based gene cloning in tomato.

Inheritance of RAPD markers in an interspecific F 1 hybrid of grape between Vitis quinquangularis and V. vinifera

Inheritance of randomly amplified polymorphic DNA (RAPD) markers in an interspecific F 1 hybrid between Vitis quinquangularis (‘83-4-96’) and V. vinifera (‘Muscat Rose’) were studied. A preliminary screen of the F 1 plants and the parents used as the interspecific cross parent was conducted with 280 RAPD primers; of these, 39 primers were polymorphic and reproducible and produced 234 scorable loci. Genomic DNA from 60 individuals of the F 1 population was then amplified with these primers; 83.4% of the loci segregated as expected in a Mendelian fashion. According to the segregation patterns, RAPD markers were grouped into three types: (1) normal Mendelian inheritance with segregation ratio of nearly 1:1, 3:1 or 1:0 (non-segregation); (2) deviation from Mendelian segregation ratios; (3) abnormal segregation in low frequency, including non-parental markers which were present in F 1 progenies but absent in both parents. RAPD markers presenting in both parents were the major source of non-segregation markers; markers presenting in only one parent mainly showed Mendelian segregation. There were five non-parental markers. Markers showing 1:1 and 3:1 segregation were used for constructing an RAPD molecular linkage map. The results demonstrated that RAPD markers could be used to study the genomes of the wild grapes native to China.

Mapping wound-response genes involved in post-harvest physiological deterioration (PPD) of cassava (Manihot esculenta Crantz)

The genome locations of the wound-response genes that were expressedduring the post-harvest physiological deterioration (PPD) of cassava, suchas phenylalanine ammonia lyase, β-1.3 glucanase, hydroxyprolinerich glycoprotein, catalase, 1-aminocyclopropane 1-carboxylate, cysteineprotease inhibitor, aspartic protease, a partial cDNA for serine/threonineprotein kinase and peroxidase, have been identified on the frameworkmolecular genetic map of cassava. Also, molecular markers linked toputative quantitative trait loci (QTLs) influencing PPD of cassava weremapped using an F1mapping population derived from elite parentallines (TMS 30572 × cm 2177-2). A molecular linkage map previouslyconstructed based on the segregation of 240 RFLP, 100 RAPD, 85microsatellite and five isoenzyme markers on 144 F1 individuals wasused for the QTL mapping.A set of 10 molecular markers with a significant association with putativeQTLs for PPD were identified based on probability values < 0.005in order to minimize the detection of false positives. Based on single-markerregression, eight putative QTLs located on the linkage groups G, P, L, U,and X of the female-derived framework map were found to explain between 5–12% of the phenotypic variance of the PPD. In the male-derived frameworkmap, two putative QTLs on linkage groups C and L explained 13% and11% of this variance, respectively. This study thus identified the majorgenome regions of cassava related to physiological post-harvestdeterioration, thereby providing tools for the identification of gene(s)controlling this trait.

Seed quality QTLs identified in a molecular map of early maturing soybean

This study identified QTLs influencing seed quality characters in a cross of two early maturing soybean (Glycine max [L.] Merr.) cultivars (Ma.Belle and Proto) adapted to the short growing seasons of Central Europe. A molecular linkage map was constructed by using 113 SSR, 6 RAPD and 1 RFLP markers segregating in 82 individuals of an F2 population. The map consists of 23 linkage groups and corresponds wellto previously published soybean maps. Using phenotypic data of the F2-derived lines grown in five environments, four markers for protein content, three for oil content and eight for seed weight were identified. Four from fifteen seed quality QTL-regions identified in the present study were also found by other authors. Markers associated with seed weight QTLs were consistent across all environments and proved to have effects large enough to be useful in a marker-assisted breeding program, whereas protein and oil QTLs showed environmental interactions.

QTL analysis of rice low temperature germinability

A double haploid population, derived from anther culture of F1 hybrid between a typicalindica and ajaponica (ZYQ8/JX17), has been used to investigate the low temperature germinability (LTG) at 15°C. The low temperature germinability of two parents was significantly different. In 6–11 d, the germination percentage of ZYQ8 was higher than that of JX17. In 12–16 d, the germination percentage of JX17 was higher than that of ZYQ8. The quantitative trait loci (QTLs) of every day for low temperature germinability have been mapped based on a molecular linkage map constructed from this population. In 8–11 d, qLTG-9 was identified in C397B-RZ617B on chromosome 9, the additive effect was positive, showing that the allele from JX17 could increase low temperature germinability. In 12–16 d, qLTG-4 was mapped between RG908 and CT563 on chromosome 4, the additive effect was negative, showing that the allele from ZYQ8 could increase low temperature germinability. These two QTLs were detected at different stages, showing the complexity of the mechanism of low temperature germinability.

Comparison of Molecular Linkage Maps and Agronomic Trait Loci between DH and RIL Populations Derived from the Same Rice Cross

Doubled haploid (DH) and recombinant inbred line (RIL) populations are two types of permanent populations for rice (Oryza sativa L.) breeding and genetic mapping. In this study, we report the comparison of molecular maps and mapped agronomic trait loci between DH and RIL populations derived from the same rice cross, ZYQ8 (indica) × JXI7 (japonica). We investigated six agronomic traits (days to heading, plant height, number of spikelets per panicle, number of grains per panicle, 1000‐grain weight, and seed set percentage) and found that five of them did not show significant differences between the two populations. Restriction fragment length polymorphism (RFLP) and microsatellite markers were selected to construct two linkage maps of the DH and RIL populations. All the DNA markers except G39 showed the same linkage groups and orders between the two populations. The genetic distance per chromosome in the RIL population was shorter than that in the DH population, and the total genetic distance of genome in the RIL population (1465 cM) was 70.5% of that in the DH population (2079 cM). In the RIL population, 27.3% markers showed distorted segregation at P &lt; 0.01 level, of which 90% markers favored indica alleles, while in the DH population, the skewed markers favoring indica and japonica alleles were in accordance with 1:1 ratio. Eight commonly distorted regions on chromosomes 1, 3, 4, 7, 8, 10, 11, and 12 were detected in both RIL and DH populations, of which seven skewed toward indica alleles and one toward japonica allele. Five of them were located near gametophytic gene loci (ga) and/or sterility gene loci (S). We also compared the quantitative trait locus (QTL) mapping results between the DH and RIL populations and found a number of similarities in the QTL locations between these two populations. So both RIL and DH populations are equally effective in rice breeding and genetic analysis.