Reciprocal Backcross Populations Research Articles

Genetic architectures of postmating isolation and morphology of two highly diverged rockfishes (genus Sebastes).

Postmating isolation is thought to be an important driver of the late stages of speciation. However, relatively little is empirically known about the process compared with other isolating mechanisms that drive the early stages of speciation, especially in non-model organisms. We characterized the genetic architecture of postmating isolation between 2 rockfishes, Sebastes schlegelii and S. trivittatus, whose reproductive isolation is complete. We examined transmission ratio distortion (TRD) patterns of genetic markers in 2 reciprocal backcross populations. Markers showing either of the 2 types of TRD was widespread across the genome, with some of the distorted markers forming extensive clusters around the recombination coldspots. These suggest that the postmating isolation effectively prevents gene flow across the genome and the recombination landscape contributes to the genetic architecture. Comparisons between 2 backcross families and 2 developmental stages showed little similarity in the distorted markers, suggesting asymmetry and stage specificity of the isolation. This may be due to hybrid incompatibility involving maternal factors or extrinsic selection. The lack of sex-ratio distortion in the mapping families suggested that Haldane's rule in terms of hybrid inviability does not hold. Additionally, quantitative trait loci (QTL) mapping detected significant QTLs for sex and the morphological traits relevant to speciation and convergence of rockfishes, including body coloration. Genes in the melanocortin system, including agouti-signaling protein 1 (asip1) and melanocortin 1 receptor (mc1r), might underlie the horizontal and vertical color patterns on the body, respectively. These findings constitute an essential step toward a comprehensive understanding of speciation and morphological diversification of rockfishes.

Wild and cultivated allele effects on rice phenotypic traits in reciprocal backcross populations between Oryza rufipogon and two cultivars, O. sativa Nipponbare and IR36.

A total of four populations of reciprocal backcross recombinant inbred lines were produced from a cross between a wild accession of Oryza rufipogon W630 and two major cultivars, O. sativa Japonica Nipponbare and Indica IR36. Using these populations, quantitative trait locus (QTL) analysis for eight morphological traits (culm length, panicle length, days to heading, panicle shape, pericarp color, hull color, seed shattering and seed awning) was carried out, and the putative QTL regions were compared among the populations. The QTLs with strong allele effects were commonly detected for culm length, panicle shape, pericarp color and hull color in all four populations, and their peak locations were close to the major genes of sd1, Spr3, Rc and Bh4, respectively. For panicle length and days to heading, some QTL regions overlapped between two or three populations. In the case of seed shattering and seed awning, strong wild allele effects at major loci were observed only in the populations with cultivated backgrounds. Since the wild and cultivated alleles have never been evaluated in the reciprocal genetic backgrounds, the present results provide new information on gene effects in breeding and domestication studies.

Genome-wide recombination variation in biparental segregating and reciprocal backcross populations provides information for introgression breeding in Brassica napus

Variation in patterns of recombination in plant genomes provides information about species evolution, genetic diversity and crop improvement. We investigated meiotic crossovers generated in biparental segregating and reciprocal backcross populations of the allopolyploid genome of rapeseed (Brassica napus) (AACC, 2n = 38). A structured set of 1445 intercrossed lines was derived from two homozygous de novo genome-assembled parents that represented the major genetic clusters of semi-winter Chinese and winter European rapeseeds, and was used to increase QTL resolution and achieve genomic reciprocal introgression. A high-density genetic map constructed with 6161 genetic bins and anchored centromere regions was used to establish the pattern of recombination variation in each chromosome. Around 93% of the genome contained crossovers at a mean rate of 3.8 cM Mb−1, with the remaining 7% attributed to centromeres or low marker density. Recombination hotspots predominated in the A genome, including two-thirds of those associated with breeding introgression from B. rapa. Genetic background might affect recombination variation. Introgression of genetic diversity from European winter to Chinese semi-winter rapeseed showed an increase in crossover rate under the semi-winter environment. Evidence for an elevated recombination rate having historically contributed to selective trait improvement includes accumulation of favorable alleles for seed oil content on hotspots of chromosome A10. Conversely, strong artificial selection may affect recombination rate variation, as appears to be the case with a coldspot resulting from strong selection for glucosinolate alleles on A09. But the cold region would be promptly reactivated by crossing design indicated by the pedigree analysis. Knowledge of recombination hotspots and coldspots associated with QTL for 22 traits can guide selection strategies for introgression breeding between the two gene pools. These results and rich genomic resources broaden our understanding of recombination behavior in allopolyploids and may advance rapeseed genetic improvement.

Recombination suppression in heterozygotes for a pericentric inversion induces the interchromosomal effect on crossovers in Arabidopsis.

SummaryDuring meiosis, recombination ensures allelic exchanges through crossovers (COs) between the homologous chromosomes. Advances in our understanding of the rules of COs have come from studies of mutations including structural chromosomal rearrangements that, when heterozygous, are known to impair COs in various organisms. In this work, we investigate the effect of a large heterozygous pericentric inversion on male and female recombination in Arabidopsis. The inversion was discovered in the Atmcc1 mutant background and was characterized through genetic and next‐generation sequencing analysis. Reciprocal backcross populations, each consisting of over 400 individuals, obtained from the mutant and the wild type, both crossed with Landsberg erecta, were analyzed genome‐wide by 143 single‐nucleotide polymorphisms. The negative impact of inversion became evident in terms of CO loss in the rearranged chromosome in both male and female meiosis. No single‐CO event was detected within the inversion, consistent with a post‐meiotic selection operating against unbalanced gametes. Cytological analysis of chiasmata in F1 plants confirmed that COs were reduced in male meiosis in the chromosome with inversion. Crossover suppression on the rearranged chromosome is associated with a significant increase of COs in the other chromosomes, thereby maintaining unchanged the number of COs per cell. The CO pattern observed in our study is consistent with the interchromosomal (IC) effect as first described in Drosophila. In contrast to male meiosis, in female meiosis no IC effect is visible. This may be related to the greater strength of interference that constrains the CO number in excess of the minimum value imposed by CO assurance in Arabidopsis female meiosis.

Identification and Characterization of Segregation Distortion Loci on Cotton Chromosome 18.

Segregation distortion is commonly detected via genetic mapping and this phenomenon has been reported in many species. However, the genetic causes of the segregation distortion regions in a majority of species are still unclear. To genetically dissect the SD on chromosome 18 in cotton, eight reciprocal backcross populations and two F2 populations were developed. Eleven segregation distortion loci (SDL) were detected in these ten populations. Comparative analyses among populations revealed that SDL18.1 and SDL18.9 were consistent with male gametic competition; whereas SDL18.4 and SDL18.11 reflected female gametic selection. Similarly, other SDL could reflect zygotic selection. The surprising finding was that SDL18.8 was detected in all populations, and the direction was skewed towards heterozygotes. Consequently, zygotic selection or heterosis could represent the underlying genetic mechanism for SDL18.8. Among developed introgression lines, SDL18.8 was introgressed as a heterozygote, further substantiating that a heterozygote state was preferred under competition. Six out of 11 SDL on chromosome 18 were dependent on the cytoplasmic environment. These results indicated that different SDL showed varying responses to the cytoplasmic environment. Overall, the results provided a novel strategy to analyze the molecular mechanisms, which could be further exploited in cotton interspecific breeding programs.

Genetic control of rhizomes and genomic localization of a major-effect growth habit QTL in perennial wildrye

Rhizomes are prostrate subterranean stems that provide primitive mechanisms of vegetative dispersal, survival, and regrowth of perennial grasses and other monocots. The extent of rhizome proliferation varies greatly among grasses, being absent in cereals and other annuals, strictly confined in caespitose perennials, or highly invasive in some perennial weeds. However, genetic studies of rhizome proliferation are limited and genes controlling rhizomatous growth habit have not been elucidated. Quantitative trait loci (QTLs) controlling rhizome spreading were compared in reciprocal backcross populations derived from hybrids of rhizomatous creeping wildrye (Leymus triticoides) and caespitose basin wildrye (L. cinereus), which are perennial relatives of wheat. Two recessive QTLs were unique to the creeping wildrye backcross, one dominant QTL was unique to the basin wildrye backcross, and one additive QTL was detectable in reciprocal backcrosses with high log odds (LOD = 31.6) in the basin wildrye background. The dominant QTL located on linkage group (LG)-2a was aligned to a dominant rhizome orthogene (Rhz3) of perennial rice (Oryza longistamina) and perennial sorghum (Sorghum propinquum). Nonparametric 99 % confidence bounds of the 31.6-LOD QTL were localized to a distal 3.8-centiMorgan region of LG-6a, which corresponds to a 0.7-Mb region of Brachypodium Chromosome 3 containing 106 genes. An Aux/IAA auxin signal factor gene was located at the 31.6-LOD peak, which could explain the gravitropic and aphototropic behavior of rhizomes. Findings elucidate genetic mechanisms controlling rhizome development and architectural growth habit differences among plant species. Results have possible applications to improve perennial forage and turf grasses, extend the vegetative life cycle of annual cereals, such as wheat, or control the invasiveness of highly rhizomatous weeds such as quackgrass (Elymus repens).

Identification and inheritance of a new source of resistance against Tomato spotted wilt virus (TSWV) in Capsicum

Tomato spotted wilt virus (TSWV) is an important viral disease affecting pepper production worldwide. A single dominant resistance gene, Tsw, originating from Capsicum chinense has been identified and utilized during the last several decades. However, there have been reports that Tsw resistance can be overcome by new field isolates of TSWV. This has necessitated the identification of a new source of resistance. Here, a set of pepper germplasm collections comprising 487 accessions from six Capsicum species and 30 commercial F1 hybrids was evaluated for resistance to TSWVPap. A new resistance source, C. chinense ‘AC09-207’, was identified and characterized. Genetic analysis showed that the resistance in C. chinense ‘AC09-207’ was conferred by a single dominant gene. The resistance responses of ‘AC09-207’ were compared with other known resistance sources. The timing and number of necrotic response were similar to C. chinense ‘PI152225’, whereas the premature abscission of inoculated cotyledons and leaves were significantly different from other resistance sources, ‘PI152225’ and ‘PI159236’. To compare genome locations between the new resistance gene and Tsw, an allelism test was conducted. No recombinants were found in all F1, F2 and reciprocal backcross populations derived from the new resistance source and three known resistance sources (‘PI152225’, ‘PI159236’, and ‘PI159234’) demonstrating that the new resistance gene may be a unique allele at the Tsw locus or be controlled by a different gene tightly linked to Tsw.

Phenotypic Correlation Among Root and Shoot Traits in an Elite Chinese Hybrid Rice Combination and Its Three Derived Populations

To elucidate the phenotypic correlations among root and shoot traits in elite hybrid rice (Oryza sativa L.), 7 root and 10 shoot traits in an RIL population of Xieyou 9308 and 2 reciprocal backcross populations (BCF1) derived from the RILs were determined under hydroponic culture and field experiment conditions. All traits, except for root diameter, panicle number per plant and grain-setting rate, were significantly different between the 2 recurrent parents, and transgressive segregations and continuous distributions were observed in either root traits or shoot traits in the RIL or BCF1 populations. In the root traits, root length was positively correlated with total root length, dry root weight, root surface area, root volume, and number of root tips; however, root diameter was negatively correlated with other root traits. In the shoot traits, heading date, plant height, panicle length, spikelet number per panicle, grain-setting density, and grain yield per plant showed significant and positive correlations with all root traits except for root diameter. These results provide applicable shoot indices for indirect selection of root traits and valuable information for super hybrid rice breeding.

Comparison of Molecular Linkage Maps and QTLs for Morphological Traits in Two Reciprocal Backcross Populations of Rice

Comparison of Molecular Linkage Maps and QTLs for Morphological Traits in Two Reciprocal Backcross Populations of Rice

Linkage analysis of the visible mutations Sel and Xan of Bombyx mori (Lepidoptera: Bombycidae) using SSR markers

Wild type silkworm larvae have opaque white skin, whereas the mutants Sel (Sepialumazine) and Xan (Xanthous) are yellow-skinned. Previous genetic analysis indicated that Sel and Xan are on established linkage groups 24 (0.0) and 27 (0.0), respectively. However, in constructing a molecular linkage map using simple sequence repeat (SSR) loci, we found that the two mutations were linked. To confirm this finding, we developed a set of SSR markers and used them to score reciprocal backcross populations. Taking advantage of the lack of crossing-over in female silkworms, we found that the progeny of backcrosses between F1 females and males of the parental strains (BC1F) of the two visible mutations had the same inheritance patterns linked to the same SSR markers. This indicated that the two visible mutations belonged to the same chromosome. To confirm this finding, we tested for independent assortment by crossing Sel and Xan marker strains with each other to obtain F1 and F2 populations. Absence of the expected wild type class among 5000 F2 progeny indicated that the two visible mutations were located on the same linkage group. We carried out recombination analysis for each mutation by scoring 190 progeny of backcrosses between F1 males and parental females (BC1M) and constructed a linkage map for each strain. The results indicated that the Sel gene was 12 cM from SSR marker S2404, and the Xan gene was 7.03 cM from SSR marker S2407. To construct a combined SSR map and to avoid having to discriminate the two similar dominant mutations in heterozygotes, we carried out recombination analysis by scoring recessive wild type segregants of F2 populations for each mutation. The results showed that the Sel and Xan genes were 13 cM and 13.7 cM from the S2404 marker, respectively, consistent with the possibility that they are alleles of the same locus, which we provisionally assigned to SSR linkage group 24. We also used the F2 recessive populations to construct two linkage groups for the Sel and Xan genes.

Identification and characterization of segregation distortion loci along chromosome 5B in tetraploid wheat

Segregation distortion genes are widespread in plants and animals and function by their effect on competition among gametes for preferential fertilization. In this study, we evaluated the segregation distortion of molecular markers in multiple reciprocal backcross populations derived from unique cytogenetic stocks involving the durum cultivar Langdon (LDN) and wild emmer accessions that allowed us to study the effects of chromosome 5B in isolation. No segregation distortion of female gametes was observed, but three populations developed to analyze segregation of male gametes had genomic regions containing markers with skewed segregation ratios. One region of distortion was due to preferential transmission of LDN alleles over wild emmer alleles through male gametes. Another region required the presence of LDN 5B chromosomes in the female for preferential fertilization by male gametes harboring LDN alleles indicating that the corresponding genes in the female gametes can govern genes affecting segregation distortion of male gametes. A third region of distortion was the result of preferential transmission of wild emmer alleles over LDN alleles through male gametes. These results indicate the existence of different distorter/meiotic drive elements among different genotypes and show that distortion factors along wheat chromosome 5B differ in chromosomal location as well as underlying mechanisms.

Pleiotropy, epistasis and new QTL: the genetic architecture of honey bee foraging behavior.

The regulation of division of labor in social insects, particularly in the honey bee (Apis mellifera L.), has received considerable attention from a number of biological subdisciplines, including quantitative and behavioral genetics, because of the high complexity of the behavioral traits involved. The foraging choices of honey bee workers can be accurately quantified, and previous studies have made the foraging behavior of honey bees one of the best studied naturally occurring behavioral phenotypes. Three quantitative trait loci (QTL) have been identified that influence a set of foraging variables, including the concentration of nectar collected and the amount of pollen and nectar brought back to the hive. This study extends previous genetic investigations and represents the most comprehensive investigation of the genetic architecture of these foraging variables. We examined the effects of markers for the three established QTL and for one further candidate gene (Amfor), in two reciprocal backcross populations. These populations were also used to carry out two new QTL mapping studies, with over 400 Amplified Fragment Length Polymorphism (AFLP) markers in each. We detected a variety of effects of the genetic markers for the established QTL and the candidate gene, which were mostly epistatic in nature. A few new QTL could be detected with a variety of mapping techniques. Our results add complexity to the genetic architecture of the foraging behavior of the honey bee. Specifically, we support the hypotheses that pln1, pln2, pln3, and Amfor are involved in the regulation of foraging behavior in the honey bee and add some new factors that deserve further study in the future.

Genetic control of susceptibility to experimental Lyme arthritis is polygenic and exhibits consistent linkage to multiple loci on chromosome 5 in four independent mouse crosses.

C3H/He mice infected with Borrelia burgdorferi develop severe arthritis and are high antibody responders, while infected C57BL/6 and BALB/c mice develop mild arthritis and less robust humoral responses. Genetic analysis using composite interval mapping (CIM) on reciprocal backcross populations derived from C3H/HeN and C57BL/6N or C3H/HeJ and BALB/cAnN mice identified 12 new quantitative trait loci (QTL) linked to 10 murine Lyme disease phenotypes. These QTL reside on chromosomes 1, 2, 4, 6, 7, 9, 10, 12, 14, 15, 16, and 17. A reanalysis of an F(2) intercross between C57BL/6N and C3H/HeN mice using CIM identified two new QTL on chromosomes 4 and 15 and confirmed the location of seven previously identified loci. Two or more experimental crosses independently verified six QTL controlling phenotypes after B. burgdorferi infection. Additionally, Bb2 on chromosome 5 was reproduced in four experimental populations and was linked to the candidate locus Cora1. Evidence of four distinct QTL residing within the 30-cM region of chromosome 5 encompassing the previously mapped Bb2 and Bb3 loci was shown by CIM. Interestingly, some alleles contributing to susceptibility to Lyme arthritis were derived from C57BL/6N and BALB/cAnN mice, showing that disease-resistant strains harbor susceptibility alleles.

Inheritance of Resistance to the NL-8 Strain of Bean Common Mosaic Necrosis Virus in Bean

Bean common mosaic necrosis virus (BCMNV) includes four African strains, BCMNV-NL3, -NL-5, -NL8, and -TN1, previously considered to be members of the bean common mosaic virus (BCMV) group. Many bean cultivars resistant to BCMNV-NL8 were found to be susceptible to the other strains of the virus. `California Light Red Kidney' (CLRK) and `Carbon', resistant to BCMNV-NL8, were crossed with the susceptible cultivars Sanilac or Black Turtle 2 (BT-2). In plants of F1, F2, and reciprocal backcross populations involving CLRK × `Sanilac' or BT-2 × `Carbon', the resistance to BCMVN-NL8 was determined to be conferred by a single dominant factor. The same factor was detected in BCMNV-NL8-resistant `Great Northern 1140' and `IVT-7214, when crossed with the susceptible cultivar Stringless Refugee or BT-2.

Developing High‐Protein, High‐Yield Soybean Populations and Lines

Developing high‐yielding, high‐protein soybean [Glycine max (L.) Merr.] lines is difficult because of the inverse relationship between seed yield and seed protein content. The objective of this study was to evaluate single cross and rapid back cross breeding methods to achieve both high seed yield and high protein content. ‘AC Proteus’ was used as the high‐protein source and ‘Maple Glen’ was used as the adapted high‐yielding parent. Six single plants were randomly selected from each of 149 F3 progeny rows to develop 886 single cross derived lines. Reciprocal back cross populations were made using 60 F1 plants from the single cross and the high‐yielding parent, Maple Glen. Ten single plant selections were randomly taken from each of 80 F1‐derived families to develop 800 back cross derived lines. In 1994, all lines were tested in the field. About 20% of lines were retained for testing through this breeding project from 1994 to 1996 although selection intensity differed across populations and years. In 1997, six single cross and nine back cross lines were tested at six locations in Eastern Canada. The seed yield and protein content of the single cross lines were not significantly different from the back cross derived lines. All the selected lines had higher seed protein content than did Maple Glen. Both breeding strategies produced lines with significantly higher seed protein content than Maple Glen. However, none of these lines had significantly higher seed yield than Maple Glen or a recently released high protein cultivar, AC Proteina. These populations exhibited a very low or no association between seed yield and protein (r = −0.06 to −0.21). Therefore, the parents may be useful sources of alleles which do not exhibit the usual pleiotrophic effect of low seed yield and high seed protein. The use of a back cross to the adapted parent following the single cross was not beneficial in the development of high yielding lines.

Molecular mapping of segregation distortion loci in Aegilops tauschii.

Distorted segregation ratios of genetic markers are often observed in progeny of inter- and intraspecific hybrids and may result from competition among gametes or from abortion of the gamete or zygote. In this study, 194 markers mapped in an Aegilops tauschii F2 population were surveyed for distorted segregation ratios. Region(s) with skewed segregation ratios were detected on chromosomes 1D, 3D, 4D, and 7D. These distorter loci are designated as QSd.ksu-1D, QSd. ksu-3D, QSd.ksu-4D, and QSd.ksu-7D. Three regions of segregation distortion identified on chromosome 5D were analyzed in two sets of reciprocal backcross populations to analyze the effect of sex and cytoplasm on segregation distortion. Extreme distortion of marker segregation ratios was observed in populations in which the F1 was used as the male parent, and ratios were skewed in favor of TA1691 alleles. There was some evidence of differential transmission caused by nucleo-cytoplasmic interactions. Our results agree with other studies stating that loci affecting gametophyte competition in male gametes are located on 5DL. The distorter loci on 5DL are designated as QSd.ksu-5D.1, QSd.ksu-5D.2, and QSd.ksu-5D.3.

Inheritance of Resistance to the Florida Strain of Zucchini Yellow Mosaic Virus in Watermelon

A high level of resistance to zucchini yellow mosaic virus (ZYMV) was found in four landraces of Citrullus lanatus (Thunb.) MatSum. & Nakai (PI 482322, PI 482299, PI 482261, and PI 482308) originally collected in Zimbabwe. This resistance is specific to the Florida strain of the virus (ZYMV-FL), which prevails in the United States. Inheritance studies were conducted by using a single-plant selection (PP261-I) of PI 48226I and the ZYMV-susceptible watermelon cultivar New Hampshire Midget. In F1, F2, and reciprocal backcross populations, resistance was conferred by a single recessive gene to which the symbol zym is assigned. There was no linkage between zym and one of the three homodimer bands of the isozyme phosphoglucoisomerase (Pgi-2b), which was found in PP261-1, and in other ZYMV-FL resistant plants.

Inheritance of resistance to peanut mottle virus in Phaseolus vulgaris

Abstract One-hundred-and-eleven bean (Phaseolus vulgaris) cultivars of domestic and foreign origin reacted identically to the N and the M strains of peanut mottle virus (PMV). Seventy-eight cultivars (70 percent) developed chlorotic or necrotlc local lesions, without systemic infection (resistant). Thirty cultivars (27 percent) were infected with local chlorotic or necrotic lesions followed by systemic necrosis and death (susceptible). Three cultivars (3 percent) yielded resistant and susceptible plants (heterogeneous populations). In F1, F2, and reciprocal backcross populations derived from crosses between PMV-resistant and -susceptible selections of the cultivar Royalty Purple Pod, resistance to the N strain was conferred by a single, but incompletely dominant gene, designated Pmv. No seed transmission of PMV could be demonstrated in progenies of susceptible cultivars because of premature death. The virus was not transmitted in seed of F2 Intermediate resistant plants.

Inheritance of Resistance to a Strain of Zucchini Yellow Mosaic Virus in Cucumber

Abstract A single plant selection of the cucumber (Cucumis sativus L.) cultivar Taichung Mou Gua (TMG-1) from China was the source of resistance to zucchini yellow mosaic virus (ZYMV) in crosses with the domestic cultivars Marketer and Marketmore 76. In F1, F2, and reciprocal backcross populations, resistance to ZYMV-CT (Connecticut strain) was demonstrated to be conferred by a single recessive gene to which the symbol zym was assigned.

Inheritance of resistance to Helminthosporium maydis blight in maize (Zea mays L.)

The nature and mode of inheritance of resistance to Helminthosporium maydis blight was investigated in two maize varieties, 'RbU-W' and 'DIC'. The study of F1, F2, and reciprocal backcross populations of crosses between these two varieties on the one hand and two susceptible varieties, 'UVE' and 'ZPSc-58c' on the other, revealed that resistance in the two varieties is monogenic recessive. The genes for resistance in the two varieties are allelic. Resistance was shown to be a lesion-type and measurements revealed that it operated through reduced lesion size and lesion number.