Analysis of genetic recombination in maize populations using molecular markers

Summary Variation in recombination rate is important to plant breeders since a major objective is to obtain favorable recombinants of linked genes. The ability to increase recombination (R) in circumstances in which favorable and unvavorable genes are linked (Corn Belt x exotic populations) and to decrease recombination when many favorable genes are linked (narrow-based, elite populations) would be of immense value. However, the concept of variation in recombination frequencies between linked genes has received limited attention despite its implications in breeding and genetic linkage studies. Molecular techniques have allowed better estimations of this variation. In this study, attempts were made to characterize: (1) the R values in the Pgm1-Adh1 and Adh1-Phi1 adjacent regions of chromosome 1 and the Idh2-Mdh2 region of chromosome 6 in F₂ families of three maize (Zea mays L.) populations; (2) the environmental effect on R values of F₂s from two populations. One population, NSO, was a Corn Belt synthetic, and the other two populations, CBMEX3 and CBCAR5, were composites from crosses between Corn Belt and exotic germ-plams.Wide ranges of estimated recombination ( ) values were observed among families in each population for all three chromsomal regions. The distribution of values for the Pgm1-Adh1 region showed that the F₂ families of each population fell into two broad categories: 0.30–0.50 and 0.02–0.20. No intermediates (0.21–0.29) were found. The distributions were almost normal for the Adh1-Phi1 and the Idh2-Mdh2 regions. It would appear that the major dispersion in the Pgm1-Adh1 region was controlled by the effects of a single gene, while the Adh1-Phi1 and Idh2-Mdh2 regions were only affected by polygenes. No correlation was found between recombination values of the two adjacent regions, indicating that the genes affecting recombination for the Pgm1-Adh1 region may be specific for that region.For the Pgm1-Adh1 region, no differences in values were found among the three populations. For the Adh1-Phi1 region, frequencies of CBMEX3 and NSO were not significantly different, but both had significantly greater values than CBCAR5. For the Idh2-Mdh2 region, CBMEX3 was significantly different from NSO. There were significant differences between some paired F₂ families within each population for each chromosome region.No significant differences in response to the two environments were detected in CBMEX3 and NSO for either region in chromosome 1.Published as Journal Paper No. 9498 of the Nebraska Agric Res Div, University of Nebraska, Lincoln, Neb. Research supported in part by USDA Competitive Grant 87-CRCR-2359     

Meiotic checkpoints and the interchromosomal effect on crossing over in Drosophila females

During prophase of meiosis I, genetic recombination is initiated with a Spo11-dependent DNA double-strand break (DSB). Repair of these DSBs can generate crossovers, which become chiasmata and are important for the process of chromosome segregation. To ensure at least one chiasma per homologous pair of chromosomes, the number and distribution of crossovers is regulated. One system contributing to the distribution of crossovers is the pachytene checkpoint, which requires the conserved gene pch2 that encodes an AAA+ATPase family member. Pch2-dependent pachytene checkpoint function causes delays in pachytene progression when there are defects in processes required for crossover formation, such as mutations in DSB-repair genes and when there are defects in the structure of the meiotic chromosome axis. Thus, the pachytene checkpoint appears to monitor events leading up to the generation of crossovers. Interestingly, heterozygous chromosome rearrangements cause Pch2-dependent pachytene delays and as little as two breaks in the continuity of the paired chromosome axes are sufficient to evoke checkpoint activity. These chromosome rearrangements also cause an interchromosomal effect on recombination whereby crossing over is suppressed between the affected chromosomes but is increased between the normal chromosome pairs. We have shown that this phenomenon is also due to pachytene checkpoint activity.     

Reversion of the Maize Mutable Allele o2-hf in Plant Ontogeny

Reversions of the mutable allele o2-hfleading to formation of the phenotypically normal kernels or whole endosperm revertants (WER) are studied in the plant ontogeny. The pattern of WER kernel distribution on the ear maps and analysis of their progeny showed that the reversion of the mutable allele o2-hf occurs at the late premeiotic stages of the ear development. Most of whole endosperm revertants on the ears homozygous for both the mutable allele o2-hfand regulatory element Bg-hf are grouped into clusters. The WER kernels are mostly formed during the period from the gamete fusion to the first division of the primary endosperm nucleus and are not embryo revertants. This clustering of revertant kernels seems to be caused by the joint effect of two factors on the early stages of endosperm development. These factors are (1) diffusion of an additional amount of transposase into the nearby Kernels from the developing endosperm, where the level of this enzyme is sufficient to induce excision of the receptor element and (2) the high proportion of the developing kernels with supra- and subthreshold levels of the Bg-hf-encoded transposase.     

Aflatoxin accumulation in preharvest maize kernels: Interaction of three fungal species,european corn borer and two hybrids

Summary The interaction was studied among: 1) developing maize kernels (Zea mays L.); 2) European Corn Borer (ECB) (Ostrinia nubilalis Hubner); 3) and three fungal species,Aspergillus flavus Lk. ex Fr.,Penicillium oxalcium Currie and Thom, andFusarium moniliforme Sheld. Two hybrids with varying degrees of resistance to ECB stalk damage were grown in Iowa, Georgia, and Missouri in 1980. One-half of the plots were hand-infested with ECB egg masses. Fungal spores of individual isolates or combinations of the three species were introduced into the silk channels of developing ears in designated plots. ECB larvae were subsequently collected from developing ears. A higher incidence ofA. flavus group isolates was observed in ECB larvae collected from ears that had been inoculated withA. flavus than from insects collected from control ears. Although the resistant hybrid exhibited reduced ECB stalk damage compared with the susceptible variety, no consistent pattern of hybrid effect on the association betweenA. flavus and ECB was observed at all three locations. Differences in aflatoxin B₁ levels in mature kernels from the three locations ranged from 8 ppb in Iowa samples to 419 ppb in Missouri kernels. Conditions during crop development at the Missouri location were particularly conducive to elevated presence ofA. flavus propagules in ECB larvae, increased ECB-mediated stalk damage, and greater toxin concentration in mature kernels.     

Differential effects of the mismatch repair genes MSH2 and MSH3 on homeologous recombination in Saccharomyces cerevisiae

The products of the yeast mismatch repair genes MSH2 and MSH3 participate in the inhibition of genetic recombination between homeologous (divergent) DNA sequences. In strains deficient for these genes, homeologous recombination rates between repeated elements are elevated due to the loss of this inhibition. In this study, the effects of these mutations were further analyzed by quantitation of mitotic homeologous recombinants as crossovers, gene conversions or exceptional events in wild-type, msh2, msh3 and msh2 msh3 mutant strains. When homeologous sequences were present as a direct repeat in one orientation, crossovers and gene conversions were elevated in msh2, msh3 and msh2 msh3 strains. The increases were greater in the msh2 msh3 double mutant than in either single mutant. When the order of the homeologous sequences was reversed, the msh2 mutation again yielded increased rates of crossovers and gene conversions. However, in an msh3 strain, gene conversions occurred at higher levels but interchromosomal crossovers were not increased and intrachromosomal crossovers were reduced relative to wild type. The msh2 msh3 double mutant behaved like the msh2 single mutant in this orientation. Control strains harboring homologous duplications were largely but not entirely unaffected in mutant strains, suggesting specificity for the mismatched intermediates of homeologous recombination. In all strains, very few (<10%) recombinants could be attributed to exceptional events. These results suggest that MSH2 and MSH3 can function differentially to control homeologous exchanges. Received: 24 December 1996 / Accepted: 24 July 1997     

Recombination rates of soybean varieties from different periods of introduction and release

Theory predicts that selection for adaptability during the short term also favors selection for a reduced recombination rate in the population. The objective of this study was to test whether the cyclic short-term selection which has taken place in soybean breeding programs in the USA since the introduction of the crop has measurably reduced recombination frequencies. Thirteen soybean varieties separated into four different release periods (prior to 1940, 1940–1954, 1955–1969, after 1970) were evaluated for their recombination frequencies within three locus pairs. Recombination frequencies among the individual varieties ranged from 7.6 to 24.1 % at thep ₁ r locus pair, from 20.9 to 30.1 % at thelnp ₂ locus pair, and from 28.7 to 41.6% at thedt ₁ l ₁ locus pair. Recombination frequencies were significantly different among varieties within a release period for thep ₁ r andlnp ₂ locus pairs, but recombination frequencies did not differ among release periods for any locus pair. Thus, apparently, plant breeders have developed soybean varieties with improved adaptation without influencing recombination rates.     

Differences between the flag leaf and the ear of a spring wheat cultivar (Triticum aestivum cv. Arkas) with respect to the CO2 response of assimilation, respiration and stomatal conductance

The CO₂- and H₂O-exchanges in the flag leaf and the ear of a spring wheat cultivar (Triticum aestivum L. cv. Arkas) were measured at CO₂ partial pressures, p_i(CO₂), between 8 and 400 Pa under high photosynthetic photon flux densities (2000 μmol m^?2 s^?1). The experiments were carried out on each organ separately while attached to the intact plant, from the time of ear emergence through senescence. To study the contribution of the kernels to the gas exchange of ears, experiments were also carried out on sterilized ears (treatment A), and on ears from which the kernels were removed (treatment B). Flag leaves and ears differed considerably with regard to CO₂-dependence of assimilation, response of stomata to varying p_a(CO₂), CO₂ compensation point (and its temperature dependence), dark respiration, and dissimilation in the light (i.e. CO₂ production which is not due to oxygenation of ribulose 1,5-bisphosphate). The higher dark respiration of the ear originated mainly from the kernels and continued to some extent in the light. Thus, the CO₂ compensation point was attained at higher CO₂ partial pressures for the ear than for the flag leaf. The CO₂ uptake of the ear was not saturated at intercellular CO₂ partial pressures below 180 Pa CO₂, while that of the flag leaf reached saturation at about 80 Pa CO₂. CO₂-saturated rates of CO₂ uptake were 2.5 and 1.5 times the rates at natural CO₂ partial pressure for ear and flag leaf, respectively. The stomatal conductance decreased with rising CO₂ partial pressure above 35 Pa, in a more pronounced manner for the flag leaf than for the ear.     

Awn contribution to gas exchanges of barley ears

The effects of awn removal on ear gas exchange in four barley lines (Morex, Harrington, Steptoe, and TR306) were studied under a controlled environment using a Before-After Control-Impact Paired (BACIP) experimental design. From ear emergence to grain maturity, plants were grown in pots at either 60 or 90 % of soil water holding capacity. Gas-exchange measurements of ears were made 9 and 10 d after anthesis (DAA). On 11 DAA, awn removal was performed on half of the ears in each pot, followed by measurements on both intact and de-awned ears on 12 and 13 DAA. Net photosynthetic (P _N) and transpiration (E) rates decreased significantly with awn removal, but dark respiration (R _D) rate was not affected. We estimated for each ear a temperature-adjusted respiration rate (R _a) from R _D. When we corrected P _N with R _a, we found that rates of spikelet photosynthesis were largely underestimated. Moderate water stress had minimal effect on gas exchange of bracts and awns of the barley ear. Barley lines did not differ for any individual gas-exchange parameter.     

Replication protein A (AtRPA1a) is required for class I crossover formation but is dispensable for meiotic DNA break repair

Replication protein A (RPA) is involved in many aspects of DNA metabolism including meiotic recombination. Many species possess a single RPA1 gene but Arabidopsis possesses five RPA1 paralogues. This feature has enabled us to gain further insight into the meiotic role of RPA1. Proteomic analysis implicated one of the AtRPA1 family (AtRPA1a) in meiosis. Immunofluorescence studies confirmed that AtRPA1a is associated with meiotic chromosomes from leptotene through to early pachytene. Analysis of an Atrpa1a mutant revealed that AtRPA1a is not essential at early stages in the recombination pathway. DNA double‐strand breaks are repaired in Atrpa1a, but the mutant is defective in the formation of crossovers, exhibiting a 60% reduction in chiasma frequency. Consistent with this, localization of recombination proteins AtRAD51 and AtMSH4 appears normal, whereas the numbers of AtMLH1 and AtMLH3 foci at pachytene are significantly reduced. This suggests that the defect in Atrpa1a is manifested at the stage of second‐end capture. Analysis of Atrpa1a/Atmsh4 and Atrpa1a/Atmlh3 double mutants indicates that loss of AtRPA1a predominantly affects the formation of class I, interference‐dependent crossovers.     

Mutation loci and intragenic selection marker of the granule-bound starch synthase gene in waxy maize

Four pairs of specific PCR primers have been designed on the basis of the sequence of the granule-bound starch synthase gene (GBSS; dominant non-waxy gene Wx) and used to amplify its homologous sequence from thirteen waxy and two non-waxy inbred lines. Results from electrophoresis indicated that the recessive waxy gene was wx, derived from the dominant non-waxy gene Wx by mutation at its 3′ end. The sequence of the mutated 3′ end was amplified by the TAIL-PCR technique. Sequence alignment showed that the mutation of the wx gene was caused by transposition of the aldehyde dehydrogenase gene rf2. Two pairs of specific primers were designed on the basis of the sequence difference between the dominant gene Wx and its mutated recessive allele wx and used as intragenic selection markers to identify individual plants of genotypes WxWx, Wxwx, and wxwx by PCR amplification from the segregating population of the F₂ generation crossed between waxy and non-waxy inbred lines. Iodine solution staining and starch component assay showed that all the 35 F₂ plants identified as genotype WxWx produced non-waxy kernels of the F₃ generation and that all 33 F₂ plants identified as genotype wxwx produced waxy kernels of the F₃ generation. This result can be used to improve the selection efficiency of waxy maize breeding and for selection of other single genes and major polygenes.     

Systemic infection of stalks and ears of corn hybrids by <Emphasis Type="Italic">Aspergillus parasiticus</Emphasis>

This study was conducted to explore systemic infection by the Aspergillus flavus group into corn ears via the stalk. An A. parasiticus mutant which produces norsolorinic (NOR) acid (a visible orange intermediate of the aflatoxin biosynthetic pathway) was used in field studies to monitor systemic infection of corn stalk and ear tissues. Corn hybrids resistant and susceptible to aflatoxin contamination were grown in the field and inoculated prior to tasseling by inserting A. parasiticus infested toothpicks into stalks between the 5th and 6th node below the lowest ear shoot. Beginning 2 weeks after inoculation, systemic infection by the NOR mutant was assessed weekly by collecting ear shank tissue and stalk tissue from the nodes between the infection sites and the developing ears. Ears were collected at the end of the growing season to determine the level of kernel infection by the NOR mutant. In two separate studies, the A. parasiticus NOR mutant was isolated from stalk tissues at all of node positions and ear shank tissue from several susceptible corn hybrid plants at the first harvest date 2 weeks after inoculation. The NOR mutant was also isolated from stalk and ear tissue of a resistant hybrid. The NOR mutant was only isolated from kernels of susceptible hybrids in 2003 and 2004. Infection rates of kernels in infected ears were very low (<1%). In 2005, the fungus was found in only one kernel from an ear of the resistant hybrid. The NOR mutant was not isolated from stalks, ears, or kernels from control (uninoculated) plants grown in the plots with inoculated plants. Although infection levels of corn kernels were low, systemic movement of the A. parasiticus up the stalk appears to be another possible route to infection of developing corn ears.     

Ear photosynthesis, carbon isotope discrimination and the contribution of respiratory CO2 to differences in grain mass in durum wheat

The role of ear photosynthesis in grain filling was studied in a number of durum wheat (Triticum turgidum var durum L.) landraces and varieties from the Middle East, North Africa, and from the collections of ‘Institut National de la Recherche Agronomique’ (INRA, France) and ‘Centro International de Mejora de Maiz y Trigo’ (CIMMYT, Mexico). Plants were grown in the field in a Mediterranean climate. Flag leaves (blade plus sheath) and ears were kept in the dark from 1 week after anthesis to maturity which reduced grain weight by 22.4% and 59.0%, respectively. In a further experiment, the carbon isotope discrimination ratio (Δ) of ear bracts, awns and flag leaves was measured on samples taken at anthesis and on mature kernels. The mean value of Δ for the water soluble fraction of bracts (17.0‰) and awns (17.7‰) were lower than those of leaves (19.5‰) and fairly similar to those of kernels (17.4‰) averaged across all genotypes. Data indicate that most of the photosynthates in the grain come from ear parts and not from flag leaves. In addition, a higher water use efficiency (WUE) of ear parts than of the flag leaf is suggested by their lower Δ values. Gas exchange in ears and flag leaves was measured during grain filling. Averaged over all genotypes, CO₂ diffusive conductance was about five times higher in the flag leaf than in the spike (with distal portions of awns outside the photosynthetic chamber) 2 weeks after anthesis. In absolute terms, the dark respiration rate (R_d) was greater than the net photosynthesis rate (P_n) by a factor of 1.74 in the spike, whereas R_d was much smaller, only 22.1, 65.7 and 24.8% of P_n in blade, sheath and awns, respectively. Data indicate that photosynthesis, and hence the water use efficiency (photosynthesis/transpiration), is greatly underestimated in ears because of the high rates of respiration which diminish the measured rates of net CO₂ exchange. Results of ¹³C discrimination and gas exchange show that genotypes from North Africa have higher WUE than those from the Middle East. The high R_d values of ears as well as their low diffusive conductance suggest that CO₂ from respiration may be used as source of carbon for ear photosynthesis. In the same way, the anatomy of glumes, for example, supports the role of bracts using internal CO₂ as source of photosynthesis. In the first experiment, the Δ in mature grains from culms with darkened ears compared with control culms provided further evidence in support of this hypothesis. Thus, the Δ from kernels of control plants was 0.40 higher than that from ear-darkened plants, probably because of some degree of refixation (recycling) of respired CO₂ in the grains.     

Repeatability and heritability of divergent recombination frequencies in the Iowa Stiff Stalk Synthetic (Zea mays L.)

Variability in recombination frequency was reported in the Iowa Stiff Stalk Synthetic. The objectives of the present research were to verify the differences in recombination frequency among individuals in the Iowa Stiff Stalk Synthetic maize population and to determine if the recombination frequency differences persisted among the S₁ progeny. Testcrosses to measure male recombination frequency on three chromosomes (4, su1-c2; 5, a2-bt1-pr1; 9, sh1-bz1-wx1) were repeated for eight S₀ individuals. Recombination frequencies were repeatably divergent among those individuals which were selected based on high or low recombination frequencies on specific chromosomes. Individuals which had been selected for long and short total map distances across the three chromosome regions produced repeatably divergent recombination frequencies only at the su1-c2 region. The recombination frequencies of the S₁ lines, derived from the S₀ individuals which had the most divergent recombination frequencies on a single chromosome, were significantly different. The broadsense heritability estimates derived from the regression of six S₁ lines on six S₀ individuals ranged from 0.69 to 0.20 for the five chromosome regions. We conclude that genetic differences for recombination frequency exist in this population and that modification by selection should be possible.     

The extent and position of homoeologous recombination in a distant hybrid of Alstroemeria: a molecular cytogenetic assessment of first generation backcross progenies

To estimate the extent and position of homoeologous recombination during meiosis in an interspecific hybrid between two distantly related Alstroemeria species, the chromosome constitution of six first generation backcross (BC₁) plants was analysed using sequential fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH) analysis. Four different probes were used for the FISH analysis: two species-specific and two rDNA probes. The six BC₁ plants were obtained from crosses between the hybrid A. aurea×A. inodora with its parent A. inodora. GISH clearly identified all chromosomes of both parental genomes as well as recombinant chromosomes. The sequential GISH and FISH analysis enabled the accurate identification of all individual chromosomes in the BC₁ plants, resulting in the construction of detailed karyotypes of the plants. The identification of the recombinant chromosomes provided evidence which chromosomes of the two species are homoeologous. Two of the BC₁ plants were aneuploid (2n=2x+1=17) and four triploid (2n=3x=24), indicating that both n and 2n gametes were functional in the F₁ hybrid. Using GISH, it was possible to estimate homeologous recombination in two different types of gametes in the F₁ hyrid. The positions of the crossover points ranged from highly proximal to distal and the maximum number of crossover points per chromosome arm was three. Compared with the aneuploid plants, the triploid plants (which received 2n gametes) clearly possessed fewer crossovers per chromosome, indicating reduced chromosome pairing/recombination prior to the formation of the 2n gametes. Besides homeologous recombination, evidence was found for the presence of structural rearrangements (inversion and translocation) between the chromosomes of the parental species. The presence of the ancient translocation was confirmed through FISH analysis of mitotic and meiotic chromosomes. Received: 7 October 1998; in revised form: 4 December 1998 / Accepted: 10 December 1998     

Effect of base pair mismatches on recombination via the RecBCD pathway

Summary The effect of base pair mismatches on recombination via the RecBCD pathway was studied in mutS and wild-type Escherichia coli, using substrates that contain single or multiple mismatches. Recombination between homologous DNA inserts in lambda phage and pBR322-derived plasmids forms phage-plasmid cointegrates that result from an odd number of crossovers. In the mutS host, when the sequence homology of a pair of 405 bp substrates decreased from 100% to 89%, the recombinant frequency decreased by about 9-fold, while in the wild-type host the decrease was about 240-fold. These results suggest that multiple mismatches can reduce recombinant frequencies by impeding the mechanism of recombination itself, and by provoking mismatch repair. Single mismatches in 31 bp substrates caused reductions in recombinant frequencies of 2-or 12-fold, depending on the location of the mismatch. However, unlike the reduction by multiple mismatches, the reduction of the recombinant frequencies by single mismatches was the same in both mutS and wild-type hosts. Thus a single match repair seems unable to act on single mismatches in very short homologies during recombination.     

Construction and analysis of a two-chromosome double reciprocal translocation that functions as a ‘balancer’ inNeurospora crassa

T(IIL; VL;IIR; VR) BLNC-1 is a compound chromosome rearrangement inNeurospora crassa that combines two reciprocal translocations:T(IIL; VL) AR30 which interchanges the left end of linkage group II with the left end of linkage group V, andT(IIR;VR) ALS154 which interchanges the right end of linkage group II with the right end of linkage group V.BLNC-1 acts as a crossover suppressor for most of both linkage groups II and V since single crossovers between the rearrangement breakpoints result in progeny with lethal unbalanced duplications and deficiencies. The integrity ofBLNC-1 following meiosis was tested in crosses of markedBLNC-1 by marked Normal sequence, with markers located at critical points on linkage groups II and V. Although recombination between distal markers in the four arms was reduced markedly, double crossovers in the long intervening regions occurred with a frequency of 21%. Of these double crossovers, most were coincidental crossovers, one in each of the long intervening regions, resulting in the resolution of the complex into its component rearrangements (16%), while a minority of the double crossovers (5%) were crossovers involving only one of the two component linkage groups, and resulted in the insertion of a segment between the breakpoints. - TheBLNC-1 balancer can be used for: (1) mapping new loci to linkage groups II and V, especially for identifying markers mapping near the tips of the linkage groups; (2) for isolating genetically intact chromosomes from natural populations or for quantitative genetic studies; and (3) for studying recombinational hot-spots which can be detected as escapes from crossover suppression. -Based on experience withBLNC-1, future two-chromosome balancers should be designed with two breakpoints near, but not at, the opposite ends of the chromosome to be balanced, and the other two breakpoints close to, but spanning, the centromere of a second chromosome. Such a construction when combined with appropriately placed selective markers should prevent breakdown of the complex, and should resemble an inversion in eliminating crossover products. Contribution no. 85-218-J from the Department of Plant Pathology, Kansas Agricultural Experiment Station, Kansas State University, Manhattan.     

Co-segregation of the maize dwarf mosaic virus resistance gene,Mdm1, with the nucleolus organizer region in maize

The mdm1 locus on the short arm of chromosome six confers resistance in maize to five strains of the maize dwarf mosaic virus (MDMV), an aphid transmitted potyvirus. The location of mdm1 in relation to RFLP and morphological loci on the short arm of chromosome six was determined using BC₁ and F₂ mapping populations. The following map order and distance in cM was obtained from the F₂ population; jc1270-2.5-npi245-1.6-umc85/po1-0.5-mdm1/nor-0.5-bnl6.29A-0.5-npi235-0.8-npi101A-4.3-numc59. No recombination between mdm1 and the nucleolus organizer region (nor) was detected, as determined using a probe from the intergenic spacer region of the rDNA repeat. In order to resolve the relationship between mdm1 and the nor, and to recover recombinants around mdm1, a highresolution map within the polymitotic1 (po1) yellow kernel1 (y1) interval was generated using [po1 y1 tester (po1 mdm1 y1) x Pa405 (Po1 Mdm1 Y1)] F₂ plants. The recessive po1 allele imparts a male-sterile phenotype when homozygous and since po1 and y1 are closely linked, the majority of fertile plants from white endosperm (y1/y1) F₂ kernels will arise though a recombination event between the Pa405 Po1 allele and the y1 allele of the po1 y1 tester. Plants from 7,650 white (y1/y1) F₂ kernels were examined (15,300 chromosomes) and a total of 626 F₂₃ recombinant families was recovered. Analysis of these recombinants revealed that mdm1 cosegregates with the nor. This lack of recombination between mdm1 and the nor suggests that: either (1) mdm1 is located in the region flanking the nor and recombination is suppressed within that region, or (2) mdm1 is located within the nor.     

Ear type in sheep is associated with the MSRB3 locus

Ear morphology is an important determinant of sheep breeds. It includes different variable traits such as ear size and erectness, suggesting a polygenic architecture. Here, we performed a comprehensive genome-wide analysis to identify regions under selection for ear morphology in 515 sheep from 17 breeds fixed for diverse ear phenotypes using 34k SNP genotyping data. GWASs for two ear type traits, size and erectness, revealed a single genome-wide significant association on ovine chromosome 3. The derived marker alleles were enriched in sheep with large and/or floppy ears. The GWAS signal harboured the MSRB3 gene encoding methionine sulphoxide reductase B3, which has already been found to be associated with different ear types in other species. We attempted whole-genome resequencing to identify causal variant(s) within a 1 Mb interval around MSRB3. This experiment excluded major copy number variants in the interval, but failed to identify a compelling candidate causal variant. Fine-mapping suggested that the causal variant for large floppy ears most likely resides in a 175 kb interval downstream of the MSRB3 coding region.     

Mutations of the Adh1 gene in maize following infection with barley stripe mosaic virus

Summary Mutations at the Adh1 locus in maize were selected from plants infected with barley stripe mosaic virus (BSMV). Pollen from the infected inbred line 1s2p, which is homozygous for Adh1-S (abbreviated S), Adh2-P, c and r was treated with allyl alcohol and applied to silks of a tester stock homozygous for Adh1-F, Adh2-N, C and R. From these pollinations 356 kernels arose on the F₁ ears. Of these eight showed no activity of the S allele in scutellar samples while two exhibited low levels. Five of the putative mutant kernels germinated and two of these contained the contamination markers Adh2-P, c and r. The newly arisen mutations were designated S5446 and S5453. S5453 exhibited an abnormally low level of ADH activity in the F₁ scutellum. In the F₂ generation the mutant reverted at a high frequency with only about 5% of the S5453 alleles expressing low levels. DNA blotting and hybridization analyses showed no alterations in the restriction patterns of S5453 when compared to the progenitor S allele. S5446 which exhibited no ADH activity in the F₁ scutellum is unstable in the pollen; reversion frequencies approaching 10^-2 were observed in samples from some plants. Restriction digestion patterns of DNA from this mutant revealed the presence of a 3.3 kb insertion at Adh. The insert does not appear to contain sequences homologous to the BSMV genome but rigorous analyses remain to be carried out. It is hypothesized that BSMV infection may mobilize endogenous but dormant transposable elements in maize.     

Genetic and physical localization of the root-knot nematode resistance locus Mi in tomato

As part of a map-based cloning strategy designed to isolate the root-knot nematode resistance gene Mi, tomato F2 populations were analyzed in order to identify recombination points close to this economically important gene. A total of 21 089 F2 progeny plants were screened using morphological markers. An additional 1887 F2 were screened using PCR-based flanking markers. Fine-structure mapping of recombinants with newly developed AFLP markers, and RFLP markers derived from physically mapped cosmid subclones, localized Mi to a genomic region of about 550 kb. The low frequency of recombinants indicated that recombination was generally suppressed in these crosses and that crossovers were restricted to particular regions. To circumvent this problem, a population of Lycopersicon peruvianum, the species from which Mi was originally introgressed, that was segregating for resistance was developed. Screening of this population with PCR, RFLP and AFLP markers identified several plants with crossovers near Mi. Recombination frequency was approximately eight-fold higher in the Mi region of the L. peruvianum cross. However, even within the wild species cross, recombination sites were not uniformly distributed in the region. By combining data from the L. esculentum and L. peruvianum recombinant analyses, it was possible to localize Mi to a region of the genome spanning less than 65 kb. Received: 15 July 1997 / Accepted: 1 October 1997