F2 Generations Of Crosses Research Articles

QTL mapping using high-throughput sequencing.

Quantitative trait locus (QTL) mapping in plants dates to the 1980s (Stuber et al. Crop Sci 27: 639-648, 1987; Paterson et al. Nature 335: 721-726, 1988), but earlier studies were often hindered by the expense and time required to identify large numbers of polymorphic genetic markers that differentiated the parental genotypes and then to genotype them on large segregating mapping populations. High-throughput sequencing has provided an efficient means to discover single nucleotide polymorphisms (SNPs) that can then be assayed rapidly on large populations with array-based techniques (Gupta et al. Heredity 101: 5-18, 2008). Alternatively, high-throughput sequencing methods such as restriction site-associated DNA sequencing (RAD-Seq) (Davey et al. Nat Rev Genet 12: 499-510, 2011; Baird et al. PloS ONE 3: e3376, 2008) and genotyping-by-sequencing (GBS) (Elshire et al. PLoS One 6: 2011; Glaubitz et al. PLoS One 9: e90346, 2014) can be used to identify and genotype polymorphic markers directly. Linkage disequilibrium (LD) between markers and causal variants is needed to detect QTL. The earliest QTL mapping methods used backcross and F2 generations of crosses between inbred lines, which have high levels of linkage disequilibrium (dependent entirely on the recombination frequency between chromosomal positions), to ensure that QTL would have sufficiently high linkage disequilibrium with one or more markers on sparse genetic linkage maps. The downside of this approach is that resolution of QTL positions is poor. The sequencing technology revolution, by facilitating genotyping of vastly more markers than was previously feasible, has allowed researchers to map QTL in situations of lower linkage disequilibrium, and consequently, at higher resolution. We provide a review of methods to identify QTL with higher precision than was previously possible. We discuss modifications of the traditional biparental mapping population that provide higher resolution of QTL positions, QTL fine-mapping procedures, and genome-wide association studies, all of which are greatly facilitated by high-throughput sequencing methods. Each of these procedures has many variants, and consequently many details to consider; we focus our chapter on the consequences of practical decisions that researchers make when designing QTL mapping studies and when analyzing the resulting data. The ultimate goal of many of these studies is to resolve a QTL to its causal sequence variation.

Genetic linkage between male sterility and non‐spiny trait in safflower (Carthamus tinctorius L.)

AbstractGenetic male sterility (GMS) exists naturally in safflower (Carthamus tinctorius L.). In the existing safflower GMS lines, sterile and fertile plants are distinguishable at flowering. This causes delay in fertile plants rouging and reduction in hybrid purity. In this investigation, a cross between a spiny GMS parent 13‐137 and a spiny non‐GMS parent ‘A1’ was effected. One sib cross, SC‐67, producing non‐parental‐type non‐spiny sterile and spiny fertile plants in F3 was advanced to F9 through sib crossing between non‐spiny sterile and spiny fertile plants. Mendelian digenic segregation was not observed for non‐spiny trait and male sterility. The results revealed strong linkage between these traits. The linkage was confirmed in F2 generations of crosses between a non‐spiny marker‐linked GMS line (MGMS) and five elite lines. Male sterility–linked non‐spiny trait could distinguish sterile and fertile plants at elongation stage. The MGMS would be useful in production of pure F1 hybrid seed and development of elite populations.

A gene influencing seed shape of desi type chickpea (Cicer arietinum L.)

With 1 figure and 1 table AbstractChickpea is an important food legume in many developing countries. Seed characteristics, especially size, shape and colour, define the two main types (‘desi’ and ‘kabuli’) and also influence the mode of consumption and economic value. We observed two distinct seed shapes in the desi breeding line 9113‐13N‐2, ‘rounded’ and ‘angular’, and sought to demonstrate a genetic basis for this difference. The mode of inheritance was studied in F1, F2 and F3 generations of crosses between rounded and angular single plant progeny from 9113‐13N‐2 and in the F2 generation of another cross between rounded and angular parents. Rounded shape was dominant to angular shape in the F1 generation, and a 3 rounded : 1 angular ratio was observed in the F2 and F3 generations. These results indicated a monogenic inheritance for seed shape in desi chickpeas. Visual differences in shape were confirmed by sphericity measurements: sphericity values for rounded seeds were significantly greater than for angular seeds. We propose the symbols Rd and rd for alleles conferring rounded and angular shape, respectively.

Gene resources for improvement of drought tolerance and yield quality in dry pea breeding

The effectiveness of selection for improved drought tolerance and consumption quality in the progeny of crosses between pea cultivars with semi-leafless (afila) and normal leaves and different origins, respectively, were investigated. After single crosses, parent cultivars and F1, F2 and F3 generations were grown under non-irrigated conditions in the same trials. We created a colour scale from 1 to 9 to measure statistically the shade of seed colour. The tolerance of genotypes against high temperature was measured by the number of pods per plant. The 3:1 segregationobserved in the F2 generation of crosses between semi-leafless and conventional cultivars indicated that the semi-leafless character is determined by a recessive gene. In contrast, the ratios of conventional (Af) and semi-leafless (af) genotypes were 7:1 and 9:1 ratio in the progenies of crosses of Af × af. The genetic progress was effective for improving the seed quality in F3 generation from crosses Af x af where we found that multipledominant alleles controlled the orange colour of cotyledons and its high heritability (h2 A=0,63). Selection is more effective in producing the genotypes with high yield and normal leaves if the crosses were made between the western European cultivars such as semi-leafless Profi and Delta used as maternal cultivars and conventional Auralia cultivars. In this case, there were decreases in the consumption quality, such as seed size and shade of colour. The selection based on the seed weight of single plants for increasing drought tolerance seemed to be more effective in F4strains with normal leaves originated from Czechoslovakian maternal cultivar Y228; however, the genetic progress in the improvement of seed size and colour quality was slow.

Hybrid Breakdown Caused by Substitution of the X Chromosome Between Two Mouse Subspecies

Abstract Hybrid breakdown is a type of reproductive failure that appears after the F2 generation of crosses between different species or subspecies. It is caused by incompatibility between interacting genes. Genetic analysis of hybrid breakdown, particularly in higher animals, has been hampered by its complex nature (i.e., it involves more than two genes, and the phenotype is recessive). We studied hybrid breakdown using a new consomic strain, C57BL/6J-XMSM, in which the X chromosome of C57BL/6J (derived mostly from Mus musculus domesticus) is substituted by the X chromosome of the MSM/Ms strain (M. m. molossinus). Males of this consomic strain are sterile, whereas F1 hybrids between C57BL/6J and MSM/Ms are completely fertile. The C57BL/6J-XMSM males showed reduced testis weight with variable defects in spermatogenesis and abnormal sperm head morphology. We conducted quantitative trait locus (QTL) analysis for these traits to map the X-linked genetic factors responsible for the sterility. This analysis successfully detected at least three distinct loci for the sperm head morphology and one for the testis weight. This study revealed that incompatibility of interactions of X-linked gene(s) with autosomal and/or Y-linked gene(s) causes the hybrid breakdown between the genetically distant C57BL/6J and MSM/Ms strains.

Hybrid breakdown caused by substitution of the X chromosome between two mouse subspecies.

Hybrid breakdown is a type of reproductive failure that appears after the F2 generation of crosses between different species or subspecies. It is caused by incompatibility between interacting genes. Genetic analysis of hybrid breakdown, particularly in higher animals, has been hampered by its complex nature (i.e., it involves more than two genes, and the phenotype is recessive). We studied hybrid breakdown using a new consomic strain, C57BL/6J-X(MSM), in which the X chromosome of C57BL/6J (derived mostly from Mus musculus domesticus) is substituted by the X chromosome of the MSM/Ms strain (M. m. molossinus). Males of this consomic strain are sterile, whereas F1 hybrids between C57BL/6J and MSM/Ms are completely fertile. The C57BL/6J-X(MSM) males showed reduced testis weight with variable defects in spermatogenesis and abnormal sperm head morphology. We conducted quantitative trait locus (QTL) analysis for these traits to map the X-linked genetic factors responsible for the sterility. This analysis successfully detected at least three distinct loci for the sperm head morphology and one for the testis weight. This study revealed that incompatibility of interactions of X-linked gene(s) with autosomal and/or Y-linked gene(s) causes the hybrid breakdown between the genetically distant C57BL/6J and MSM/Ms strains.

Saturated fatty acid content in sunflower seed

RSI and RS2 are two genetic stocks that have low saturated fatty acid (SFA) contents. In this two-year study, we report on the inheritance of palmitic and stearic acids of RSI and RS2 in the F1 and F2 generations of crosses with HA 382, an inbred line with a fatty acid composition similar to many commercial sunflower hybrids. The expression of the reduced palmitic and stearic acid traits is most important in the F2 generation because it is the F2 seed that is harvested by the farmer, sold, and crushed for the oil. Our experiments showed that the F2 seed of reciprocal crosses of RSI or RS2 with HA 382 was intermediate in SFA content between the two hybrid parents. The inheritance and expression of the reduced palmitic and stearic acid traits of RS1 and RS2 were controlled by more than one gene. In addition, there were significant relative changes in palmitic and stearic acid contents between the growing seasons of 2002 and 2003, suggesting that environment played a significant role in the relative proportions of these fatty acids. The total SFA content was also influenced by environment, producing opposite effects with RSI (higher total SFA in 2003) and RS2 (lower total SFA in 2003). The data demonstrate that it will be necessary to incorporate the reduced SFA trait into both parents of a hybrid in order to achieve the lowest concentration of SFAs in the F2 seed.

Genetic control and chromosomal location of Triticum timopheevii-derived resistance to septoria nodorum blotch in durum wheat

The genetic control of resistance, expressed as restricted lesion development in seedling plants, to septoria nodorum blotch of wheat was studied under controlled environmental conditions, using the parental, F1, F2, F3, BC1F1, and BC1F2 generations of crosses of Triticum timopheevii-derived resistant durum lines S3-6, S9-10, and S12-1 with the susceptible durum cv. Sceptre. The seedling resistance of these three resistant sources, derived from T. timopheevii (PI 290518), was monogenically controlled. The chromosomal location of the resistance gene identified was determined by crossing the complete set of 'Langdon' - 'Chinese Spring' D-genome disomic substitution lines with S12-1. Tests of the F1 and F2 generations of each cross indicated that only chromosome 3A was associated with resistance. Therefore, the resistance gene is considered to be located on chromosome 3A and has been designated temporarily as SnbTM.

Complementarity of genes for resistance to greenbug [Schizaphis graminum (Rondani)], biotype E, in sorghum [Sorghum bicolor (L.) Moench

Gene complementarity among various sources of resistance to greenbug biotype E was assessed. Analysis of the F2 generation of crosses between susceptible and resistant parents (mating 1) and among sources of resistance (mating 2) suggested that resistance in sorghum to greenbug biotype E was complexly inherited and, to some extent, dependent on the nature of both the resistant and susceptible parents. Positive transgressive segregation in the F2 generations of both matings was found to be due to effective plus factors, contributed by both parents in a cross, which complemented each other. The number of plus factors ranged from one to two in the susceptible parents and from two to five in the resistant parents of mating 1, and from one to five in the parents of mating 2. The consistently significant reciprocal effects shown by Sarvasi and PI264453 indicated that these sources had major factors for resistance in their cytoplasms, which were expressed in all their crosses. The results from this study indicated that the sources of resistance complemented each other to give increased number of F2 segregates with increased resistance. Thus, it should be possible to increase and diversify resistance of sorghum to greenbug biotype E by accumulating different, effective plus factors from various sources through recurrent selection.

Independent Inheritance of Flower Colour and Male‐Fertility Restorer Characters in Brassica napus L.

AbstractAvailable material of oilseed (Brassica napus L., AACC) comprises two yellow‐flowered breeding lines and a white/pale‐flowered line of resynthesized rape. The flower colour white/pale is dominant over yellow, and is controlled by a gene located in the C‐genome. The yellow‐flowered genotypes acted as restorer lines and the white/pale‐flowered genotype as a maintainer line in a cytoplasmic male sterility system. The segregation pattern of flower colour and male fertility restorer characters were studied in F2 generations of crosses between these lines, also in a three‐way cross additionally including a yellow flowered B. campestris (AA) line. Evidense was obtained in support of the conclusion that the flower colour and male fertility restorer characters are monogenically controlled and independently inherited. Whether the male fertility restorer gene is located in the A or C genome remains to be determined.

Asp 8271 and Asp 8284 Asparagus Germplasm

Abstract Asparagus germplasm populations, Asp 8271 and Asp 8284, are the F2 generation of crosses between colchicine-induced tetraploids of garden asparagus, Asparagus officinalis L. ‘Viking’, and a wild tetraploid, A. officinalis spy. prostratus (Dumort.) Corb., both 2n = 4x = 40. They were released in Feb. 1987 from a program at Beltsville in which crosses in the genus are investigated as they relate to the gene pool available for breeding disease-resistant garden asparagus.

Stability of a two-locus ‘coacting’ cline in Silene latifolia: A model study

A gene oriented model was used to study a transition zone between two chemical races of Silene latifoliain western Europe, in which a two-locus cline of ‘coacting’ flavone glycosylation loci occurs: i.e. each locus contributes to this glycosylation. In the F2 generation of crosses between these two chemical races, each homozygous dominant for one of these loci, plants arise which are homozygous recessive for both of these loci. These plants are inactive in flavone glycosylation and hence have a reduced fitness. We show that this F2 hybrid unfitness, unlike a single locus F1 hybrid unfitness, is not able to generate a stable cline. Adding a very small selection against the recombinant which is homozygous dominant on both loci, however, gives rise to stability. Biological implications are discussed.

Genetics of formamidase-5 (brain formamidase) in the mouse: localization of the structural gene on chromosome 14.

A single formamidase, which is different from the formamidases found in other tissues occurs in the brains of mice. This enzyme is here called formamidase-5 and the gene symbol is designated For-5. Two alleles are recognized on the basis of their differential heat sensitivity:For-5b is relatively heat stable and is present in strain C57BL/6J, while For-5d is relatively heat sensitive and is present in strain DBA/2J. The heat sensitivity of formamidase-5 in 44 other inbred strains and substrains was tested and found to resemble that of C57BL/6J or DBA/2J. Thirty-six recombinant inbred strains derived from progenitors that differed at For-5 were studies to test for single-gene inheritance and linkage with other loci. Complete concordance was found with the esterase-10 locus (Es-10), indicating close linkage. The 99% upper confidence limit of the distance between For-5 and Es-10 is 3.7 centimorgans (cM). Es-10 is located on chromosome 14 about 19 cM from the centromere. An independent demonstration of linkage of For-5 with Es-10 and another chromosome 14 marker, hairless (hr), is provided by the finding that the HRS/J strain, which has been sibmated for 60 generations with forced heterozygosity at the hr locus, is cosegregating at For-5 and Es-10. A survey of 32 inbred strains and substrains revealed that the For-5d allele is associated with the Es-10b allele, and that the For-5b allele is associated with Es-10a and Es-10c. Formamidase-5 segregates as expected in the F2 generation of crosses between strains bearing For-5b and For-5d alleles. It is possible that this unique formamidase of the brain is involved in the metabolism of a neurotransmitter substance.

Glk: A locus controlling galactokinase activity in the mouse

Inbred strains of mice exhibited significant variation in whole blood galactokinase (GALK) activity. Activities tend to cluster into two classes, one class having approximately twice the activity of the other. Hybrids (F1) between "high" and "low" strains have activity intermediate between the parental activities. Two sets of recombinant inbred (RI) lines were developed by brother-sister mating, beginning with F2 generations of crosses between different pairs of high and low GALK activity strains. The RI lines segregated in terms of GALK activity, indicating single gene inheritance; this galactokinase locus has been designated Glk. The strain distribution patterns of both RI series agreed closely with esterase-3 (Es-3) alleles of the respective parental strains (31/34 independently derived strains were concordant for Es-3 and Glk genotypes), a finding consistent with a map distance between loci of 2.5 cM. Es-3 has been located on the distal end of chromosome 11. Glk, with its alleles Glka (lower activity) and Glkb (higher activity), is therefore assigned to the same region.

Resistance of tomato cultivars and progenies to fruit hollowness

In field experiments with fall and winter tomatoes, the incidence of fruit hollowness was found to range from 0 to more than 80%, depending both on the cultivar and the environment. The most resistant cultivars were Bonner Beste and Potentate; the most susceptible were Exhibiton, Moneymaker, E.S. 1, Berco, Cromco and Ailsa Craig. The rate of hollowness of F1 and F2 generations of crosses between resistant and susceptible parents suggests that resistance behaves as a partially dominant character governed by a small number of genes. Thus, commercial F1 hybrids resistant to the disorder are easy to produce. The heritability of the resistance character was found to be rather high.

The inheritance of marker genes in Medicago truncatula Gaertn. II. Their suitability for the use in a plant breeding programme

In the F2 generation of crosses between selected strains of Medicago truncatula Gaertn. there was independent segregation of the genes for the marker characters "red leaf", "smooth pod", and "clockwise-anticlockwise coiling pattern of the pod". A new marker, "erect type" of vegetative development, is a recessive character which is not linked to the "red leaf" gene. The absence of linkage greatly enhances the value of these characters as strain markers.

The inheritance of bean size, pod size and number of beans per pod in cocoa (Theobroma cacao L.), with a note on bean shape

Studies have been made on the F1 and F2 generations of crosses between the Amazon clones Nanay 32, Parinari 7, and Parinari 35. There is wide variation in size from pod to pod on a tree, and this is largely paralleled by variation in bean number, bean size remaining relatively constant. However in some trees bean size increases in the largest pods, bean number remaining constant. It appears that if a pod is too small for the inherent number of beans to be present at their inherent size, the number of beans which develop is reduced so that their inherent size is attained; if the pod is larger than is required for the full number of beans to attain their inherent size the beans may increase in size above the inherent value. Thus if the average bean size in a sample of pods taken from a tree indicates the inherent bean size reasonably accurately it is likely that the inherent bean number will be relatively underassessed, and conversely if the observed bean number indicates the inherent number relatively accurately it is likely that the observed bean size will overassess the inherent size. Scatter-diagrams may therefore be more informative than averages.

Studies on the mechanism of flower colour formation. IV. : The appearance of variegation.

It has been reported by rhany investigators that the appearance of variegation in the petal was the somatic mutation of mutable gene. In spite of the mutation rate of the gene changing under different enviromental conditions, the physiological meaning of the mutability has, not yet been clarified. These experiments have been carried out to study the appearance of variegation from the standpoint of physiological genetics in Petunia hybrida. . As variegated plants generally segregate in F2 generation of crosses between cyanic and acyanic strains and offsprings. of the variegated plant s, egregate into the coloured and white in the ratio 3 : 1, it is believed that the genotype of variegated plant is heterozygous for E gene, which controls the activity of polyphenol oxydase. However, the s.egregation ratio comes off so often from I full coloured : 2 variegated : I white in the offsprings of variegated plant and I variegated : I white in backcross. The ratio of variegated appearance also differs in parent and filial screnerations. Then, the variegation appears as a result of the somatic mutation of E gene. The mutation must bc occuring by the reduction of activity of polyphenol oxydase as proved by the enzyme distribution.

CHARACTER COMBINATIONS IN RELATION TO ENDOSPERM DEVELOPMENT IN INTER-SPECIFIC TRITICUM CROSSES

A study was made of the frequency of different character combinations in relation to seed plumpness in the F2 generation of crosses of T. durum, T. dicoccum and T. persicum with T. vulgare. Some inter-specific character combinations occurred frequently and others were rare, which was expected since the characters varied markedly in their frequency of inter-specific combinations with other characters. The data did not support the popular assumption that inter-specific character combinations of value were to be found largely in plants from shrunken seeds rather than in those from plump seeds. Plants from plump seeds possessed nearly as large a proportion of the combinations which were missing in the plants from shrunken seeds as did the latter plants with respect to the former. The difference could not be considered significant and none of the missing combinations appeared to be important as far as practical breeding is concerned.

Studies in the Inheritance of Disease Resistance. II

The F2 generation of crosses between a number of varieties of wheat susceptible to the attacks of Yellow Rust (Puccinia glumarum) and “American Club.” which shows an extraordinary degree of resistance to the attacks of this parasite showed in the year 1906 obvious segregation into immune and susceptible forms. The immunity was further found to be independent of any recognizable morphological feature. An analysis of these F2 generations demonstrated the fact that the immune plants were present to the extent of 25 per cent., that is that the property of resisting the attacks of Yellow Rust behaves as a recessive character to the property of being susceptible. The plants which proved susceptible showed, however, very varied degrees of susceptibility. Many were as covered with rust pustules as Michigan Bronze, one of the extremely susceptible varieties used as a parent. Others on the other hand were relatively slightly attacked and between these extremes all degrees of susceptibility appeared to exist. Nilsson-Ehle who has also observed the segregation of this pair of characteristics has also noted the wide differences in susceptibility in plants of the F2 and succeeding generations.