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Detection of nitrogen deficiency QTL in juvenile wild barley introgression lines growing in a hydroponic system.

Hoffmann A, Maurer A, Pillen K - BMC Genet. (2012)

Bottom Line: The post-hoc Dunnett test identified 28 S42ILs that revealed significant (P < 0.01) effects for at least one trait.Forty-three, 41 and 42 S42ILs revealed effects across both N treatments, under low N and under high N treatment, respectively.Due to this finding, screening of plants in early developmental stages grown in a hydroponic system may be a fast and cost effective method for early QTL detection and marker-assisted allelic selection, potentially speeding up elite barley breeding programs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str, 3, Halle, 06120, Germany.

ABSTRACT

Background: In this report we studied the genetic regulation of juvenile development of wild barley introgression lines (S42ILs) under two contrasting hydroponic nitrogen (N) supplies. Ten shoot and root related traits were examined among 42 S42ILs and the recurrent parent 'Scarlett'. The traits included tiller number, leaf number, plant height, leaf and root length, leaf to root length ratio, shoots and root dry weight, shoot to root weight ratio, and chlorophyll content. Our aims were (1) to test the suitability of a hydroponic system for early detection of favourable S42ILs, (2) to locate quantitative trait loci (QTL) that control the examined traits, (3) to identify favourable wild barley alleles that improve trait performances in regard to N treatment and, finally, (4) to validate the identified QTL through comparison with previously reported QTL originating from the same parental cross.

Results: The phenotypic data were analysed in a mixed model association study to detect QTL. The post-hoc Dunnett test identified 28 S42ILs that revealed significant (P < 0.01) effects for at least one trait. Forty-three, 41 and 42 S42ILs revealed effects across both N treatments, under low N and under high N treatment, respectively. Due to overlapping or flanking wild barley introgressions of the S42ILs, these associations were summarised to 58 QTL. In total, 12 QTL of the hydroponic N study corresponded to QTL that were also detected in field trials with adult plants of a similar S42IL set or of the original S42 population. For instance, S42IL-135, -136 and -137, revealed increasing Hsp effects for tiller number, leaf number, leaf length, plant height and leaf to root ratio on the long arm of chromosome 7H. These QTL correspond to QTL for ears per plant and plant height that were previously detected in field trials conducted with the same S42ILs or with the S42 population.

Conclusion: Our results suggest that the QTL we identified under hydroponic N cultivation partly correspond to QTL detected in field experiments. Due to this finding, screening of plants in early developmental stages grown in a hydroponic system may be a fast and cost effective method for early QTL detection and marker-assisted allelic selection, potentially speeding up elite barley breeding programs.

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SNP map with 58 significant (P <0.01) QTL effects among 42 S42ILs and nine traits. The chromosomes 1H to 7H are indicated as grey bars. The centromeric region is indicated as a black box within the chromosome. The cM positions of the SNP loci are indicated with the ruler at the bottom, according to Schmalenbach et al.[19]. The extent of the target Hsp introgression of each S42IL is given above the respective chromosome. Homozygous Hsp loci, heterozygous Hsp loci and loci without SNP data are presented in red, pink and light grey, respectively. The associated QTL effects are indicated right to the introgressions with abbreviations of the nine traits, i.e. TN, LN, LL, HEI, SDW, RL, RDW, LRR, SRR. Trait abbreviations are explained in Table2. The colour of the abbreviations indicates an increasing (red) or decreasing (blue) Hsp effect. Highly significant (P < 0.001) associations are highlighted with an asterisk. Trait associations that were only detected under one treatment are labelled with N100 or N25, respectively.
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Figure 1: SNP map with 58 significant (P <0.01) QTL effects among 42 S42ILs and nine traits. The chromosomes 1H to 7H are indicated as grey bars. The centromeric region is indicated as a black box within the chromosome. The cM positions of the SNP loci are indicated with the ruler at the bottom, according to Schmalenbach et al.[19]. The extent of the target Hsp introgression of each S42IL is given above the respective chromosome. Homozygous Hsp loci, heterozygous Hsp loci and loci without SNP data are presented in red, pink and light grey, respectively. The associated QTL effects are indicated right to the introgressions with abbreviations of the nine traits, i.e. TN, LN, LL, HEI, SDW, RL, RDW, LRR, SRR. Trait abbreviations are explained in Table2. The colour of the abbreviations indicates an increasing (red) or decreasing (blue) Hsp effect. Highly significant (P < 0.001) associations are highlighted with an asterisk. Trait associations that were only detected under one treatment are labelled with N100 or N25, respectively.

Mentions: Our investigations on juvenile barley plants in a hydroponic system were carried out with introgression lines (ILs) of the population S42IL. The S42ILs are derived from a cross between the German spring barley (Hv) cultivar ‘Scarlett’ and the Israeli wild barley (Hsp) accession ‘ISR42-8’. Advanced backcrossing with ‘Scarlett’ and marker assisted selection with SSRs resulted in the development of a set of 59 S42ILs in BC3S4 generation as described in Schmalenbach et al.[13]. Based on genotypic data with 636 informative SNPs[19] we selected 42 representative S42ILs with target introgressions located on chromosomes 1H to 7H (Figure1). The recurrent parent ‘Scarlett’ served as the control genotype in the hydroponic experiments conducted.


Detection of nitrogen deficiency QTL in juvenile wild barley introgression lines growing in a hydroponic system.

Hoffmann A, Maurer A, Pillen K - BMC Genet. (2012)

SNP map with 58 significant (P <0.01) QTL effects among 42 S42ILs and nine traits. The chromosomes 1H to 7H are indicated as grey bars. The centromeric region is indicated as a black box within the chromosome. The cM positions of the SNP loci are indicated with the ruler at the bottom, according to Schmalenbach et al.[19]. The extent of the target Hsp introgression of each S42IL is given above the respective chromosome. Homozygous Hsp loci, heterozygous Hsp loci and loci without SNP data are presented in red, pink and light grey, respectively. The associated QTL effects are indicated right to the introgressions with abbreviations of the nine traits, i.e. TN, LN, LL, HEI, SDW, RL, RDW, LRR, SRR. Trait abbreviations are explained in Table2. The colour of the abbreviations indicates an increasing (red) or decreasing (blue) Hsp effect. Highly significant (P < 0.001) associations are highlighted with an asterisk. Trait associations that were only detected under one treatment are labelled with N100 or N25, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3584942&req=5

Figure 1: SNP map with 58 significant (P <0.01) QTL effects among 42 S42ILs and nine traits. The chromosomes 1H to 7H are indicated as grey bars. The centromeric region is indicated as a black box within the chromosome. The cM positions of the SNP loci are indicated with the ruler at the bottom, according to Schmalenbach et al.[19]. The extent of the target Hsp introgression of each S42IL is given above the respective chromosome. Homozygous Hsp loci, heterozygous Hsp loci and loci without SNP data are presented in red, pink and light grey, respectively. The associated QTL effects are indicated right to the introgressions with abbreviations of the nine traits, i.e. TN, LN, LL, HEI, SDW, RL, RDW, LRR, SRR. Trait abbreviations are explained in Table2. The colour of the abbreviations indicates an increasing (red) or decreasing (blue) Hsp effect. Highly significant (P < 0.001) associations are highlighted with an asterisk. Trait associations that were only detected under one treatment are labelled with N100 or N25, respectively.
Mentions: Our investigations on juvenile barley plants in a hydroponic system were carried out with introgression lines (ILs) of the population S42IL. The S42ILs are derived from a cross between the German spring barley (Hv) cultivar ‘Scarlett’ and the Israeli wild barley (Hsp) accession ‘ISR42-8’. Advanced backcrossing with ‘Scarlett’ and marker assisted selection with SSRs resulted in the development of a set of 59 S42ILs in BC3S4 generation as described in Schmalenbach et al.[13]. Based on genotypic data with 636 informative SNPs[19] we selected 42 representative S42ILs with target introgressions located on chromosomes 1H to 7H (Figure1). The recurrent parent ‘Scarlett’ served as the control genotype in the hydroponic experiments conducted.

Bottom Line: The post-hoc Dunnett test identified 28 S42ILs that revealed significant (P < 0.01) effects for at least one trait.Forty-three, 41 and 42 S42ILs revealed effects across both N treatments, under low N and under high N treatment, respectively.Due to this finding, screening of plants in early developmental stages grown in a hydroponic system may be a fast and cost effective method for early QTL detection and marker-assisted allelic selection, potentially speeding up elite barley breeding programs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str, 3, Halle, 06120, Germany.

ABSTRACT

Background: In this report we studied the genetic regulation of juvenile development of wild barley introgression lines (S42ILs) under two contrasting hydroponic nitrogen (N) supplies. Ten shoot and root related traits were examined among 42 S42ILs and the recurrent parent 'Scarlett'. The traits included tiller number, leaf number, plant height, leaf and root length, leaf to root length ratio, shoots and root dry weight, shoot to root weight ratio, and chlorophyll content. Our aims were (1) to test the suitability of a hydroponic system for early detection of favourable S42ILs, (2) to locate quantitative trait loci (QTL) that control the examined traits, (3) to identify favourable wild barley alleles that improve trait performances in regard to N treatment and, finally, (4) to validate the identified QTL through comparison with previously reported QTL originating from the same parental cross.

Results: The phenotypic data were analysed in a mixed model association study to detect QTL. The post-hoc Dunnett test identified 28 S42ILs that revealed significant (P < 0.01) effects for at least one trait. Forty-three, 41 and 42 S42ILs revealed effects across both N treatments, under low N and under high N treatment, respectively. Due to overlapping or flanking wild barley introgressions of the S42ILs, these associations were summarised to 58 QTL. In total, 12 QTL of the hydroponic N study corresponded to QTL that were also detected in field trials with adult plants of a similar S42IL set or of the original S42 population. For instance, S42IL-135, -136 and -137, revealed increasing Hsp effects for tiller number, leaf number, leaf length, plant height and leaf to root ratio on the long arm of chromosome 7H. These QTL correspond to QTL for ears per plant and plant height that were previously detected in field trials conducted with the same S42ILs or with the S42 population.

Conclusion: Our results suggest that the QTL we identified under hydroponic N cultivation partly correspond to QTL detected in field experiments. Due to this finding, screening of plants in early developmental stages grown in a hydroponic system may be a fast and cost effective method for early QTL detection and marker-assisted allelic selection, potentially speeding up elite barley breeding programs.

Show MeSH
Related in: MedlinePlus