Browsing by Subject "Genetics"

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Dietary phosphorus and calcium in feed affects miRNA profiles and their mRNA targets in jejunum of two strains of laying hens
(2021) Iqbal, Muhammad Arsalan; Ali, Asghar; Hadlich, Frieder; Oster, Michael; Reyer, Henry; Trakooljul, Nares; Sommerfeld, Vera; Rodehutscord, Markus; Wimmers, Klaus; Ponsuksili, Siriluck
Phosphorus (P) and calcium (Ca) are critical for egg production in laying hens. Most of P in plant-based poultry diet is bound as phytic acid and needs to be hydrolysed before absorption. To increase P bioavailability, exogenous phytases or bioavailable rock phosphate is added in feed. There is growing evidence of the importance of miRNAs as the epicentre of intestinal homeostasis and functional properties. Therefore, we demonstrated the expression of miRNA profiles and the corresponding target genes due to the different levels of P (recommended vs. 20% reduction) and/or Ca (recommended vs. 15% reduction) in feed. Jejunal miRNA profiles of Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) laying hens strains were used (n = 80). A total of 34 and 76 miRNAs were differentially expressed (DE) in the different diet groups within LSL and LB strains respectively. In LSL, the DE miRNAs and their targets were involved in calcium signaling pathway, inositol phosphate metabolism, and mitochondrial dysfunction. Similarly, in LB miRNAs targets were enriched in metabolic pathways such as glutathione metabolism, phosphonate metabolism and vitamin B6 metabolism. Our results suggest that both strains employ different intrinsic strategies to cope with modulated P and Ca supply and maintain mineral homeostasis.
Gene mining in doubled haploid lines from European maize landraces with association mapping
(2014) Strigens, Alexander Carl Georg; Melchinger, Albrecht E.
Since the introduction of maize into Europe, open-pollinated varieties of flint maize were cultivated across the continent. Natural selection promoted adaptation to the climatic conditions prevailing in the different regions. With the advent of hybrid breeding in Europe during the 1950’s, some of the genes responsible for the specific adaptations of the landraces to abiotic and biotic stress were captured in the first developed inbred lines, but most of their genetic diversity is still untapped. Development of inbred lines out of this material by recurrent selfing is very tedious due to strong inbreeding depression. In contrast, the doubled-haploid (DH) technology allows producing fully homozygous lines out of landraces in only one step. This allows their precise characterization in replicated trials and identification of new genes by genome wide association (GWA) mapping. In this study we genotyped a set of 132 DH lines derived from European Flint landraces and 364 elite European flint (EU-F), European dent (EU-D) and North-American dent (NA-D) inbred lines with 56,110 single nucleotide polymorphism (SNP) markers. The lines were evaluated in field trials for morphologic and agronomic traits and GWA mapping was performed to identify underlying quantitative trait loci (QTL). In particular, our objectives were to (1) develop a robust method for quantifying early growth with a non-destructive remote-sensing platform, (2) evaluate the importance of early growth performance of inbred lines with regard to their testcross performance, (3) determine the potential of GWA mapping to identify genes underlying early growth and cold tolerance related traits, (4) evaluate the phenotypic and genotypic diversity recovered in the DH lines derived from the landraces, (5) estimate the effect of the DH method on the recovered genetic diversity, (6) identify new genes by GWA mapping in the DH lines derived from landraces, and (8) discuss the potential of DH lines derived from landraces to improve the genetic diversity and performance of elite maize germplasm. A phenotyping platform using spectral reflectance and light curtains was used to perform repeated measurements of biomass and estimate relative growth rates (RGR) of the DH and inbred lines, as well as of two testcrosses of 300 dent inbred lines. The DH lines derived from the landraces Schindelmeiser and Gelber Badischer had the highest RGR followed by EU-F lines, DH lines derived from Bugard, EU-D lines and, finally, NA-D lines. For inbred lines, whole plant dry matter yield (DMY) was positively correlated with RGR (r = 0.49), whereas this relation was weaker in the testcrosses (r = 0.29). RGR of the inbred lines correlated with RGR of their testcrosses (r = 0.42), but it had no influence on testcross DMY. A set of 375 EU-F, EU-D and NA-D lines were further evaluated in growth chambers under chilling (16/13°C) and optimal (27/25°C) temperatures. Photosynthetic and early growth performance were estimated for each treatment and an adaptation index (AI) built as the chilling to optimal performance ratio. Nineteen QTL were identified by GWA mapping for trait performance and AI. Candidate genes involved in ethylene signaling, brassinolide, and lignin biosynthesis were found in their vicinity. Several QTL for photosynthetic performance co-located with previously reported QTL and the QTL identified for shoot dry wieght under optimal conditions co-located with a QTL for RGR. Comparison of the DH lines derived from landraces with the EU-F lines showed that genotypic variances in single DH populations were greater than in the EU-F breeding population. A high average genetic distance among the DH lines derived from the same landrace as well as a rapid decay of linkage disequilibrium suggests a high effective population size of the landraces. Because no systematic phenotypic differences were observed between the landraces and synthetic landraces obtained by intermating the corresponding DH lines, the expected purge of lethal recessive alleles during the DH production did neither improve grain yield performance nor affect the recovered genetic diversity. Performing GWA in the DH lines derived from landraces as well as the EU-F, and EU-D lines allowed the identification of 49 QTL for 27 traits. A larger set of DH lines derived from more landraces might solve problems arising from population structure and allow a much higher power for the detection of new alleles. In conclusion, the introgression of DH lines derived from landraces into the elite breeding material would strongly broaden its genetic base. However, grain yield performance was 22% higher in EU-F lines than in the DH lines derived from landraces. Selection of the best DH lines would allow partially bridging this yield gap and marker-assisted selection may allow introgression of positive QTL without introducing negative features by linkage drag.
Genetic architecture of quality traits in wheat
(2021) Rapp, Matthias; Longin, Friedrich
Quality traits in wheat are of great importance, as they are required for the production of a wide range of food products. In Europe, bread wheat (Triticum aestivum ssp. aestivum) for human consumption is primarily used in pastries. For durum wheat (Triticum turgidum ssp. durum) that is used almost exclusively for pasta production, quality traits are at least as important as in bread wheat. In Central Europe, the bread wheat subspecies spelt (Triticum aestivum ssp. spelta) is characterized by a different quality compared to bread wheat. In addition, it is produced for a niche market with a particular focus on the final product quality. The high number of demanded quality traits of a wheat variety represents a great challenge for wheat breeders. Thus, knowledge about the genetic architecture and interrelation of quality traits is of high value for wheat breeding. Due to the long list of quality traits in wheat, we focused on currently important quality traits in each of the three wheat species. In durum wheat, I was interested in traits with a high importance for durum millers and pasta producers. The protein content and the sedimentation volume are of high importance for pasta producers as they influence the firmness of cooked pasta, better known as “al dente”. A low falling number may lead to brown instead of light yellow pasta, which goes back to an increased maillard reaction during pasta production and drying. The vitreousity, representing the glassy appearance of durum grains, and the thousand kernel mass influence the semolina yield and are therefore of great interest for durum millers. In the genome-wide association mapping, I identified several putative QTL for these quality traits. For the sedimentation volume, a genomic region on chromosome 1B appeared to be important. A BLAST search against the reference genomes of emmer and bread wheat revealed the Glu-B3 gene as a likely candidate. For vitreousity, genomic regions on chromosome 7A explained a larger proportion of the genotypic variance. One of these QTL, possibly related to the Pinb-2 locus, also slightly influenced the protein content. Thus, this genomic region might be a genomic reason for the positive correlation between vitreousity and protein content. For TKM we detected a putative QTL, which explained a large proportion of the genetic variance, but could not be attributed to a known gene. Besides a good performance for quality traits, a modern durum wheat variety should be complemented by a good agronomic performance, in particular a high grain yield. This poses a great challenge for plant breeders, since grain yield and protein content are negatively correlated. With regard to simultaneously improving grain yield and protein content, the protein yield or the grain protein deviation (GPD) were proposed. We evaluated those and further selection indices for their potential to be utilized for the simultaneous improvement of grain yield and protein content. Our results indicated that a simultaneous improvement of the two traits grain yield and protein content by means of an index seems possible. However, its efficiency largely depends on the weighting of the single traits. The selection for a high GPD would mainly increase the protein content whereas a selection based on protein yield would mainly improve the grain yield. Nevertheless, a combination of different indices allows balancing this selection. Compared to the primary traits grain yield and protein content, the selection indices did not essentially differ in the complexity of their genetic architecture. In bread wheat, we focused on the acrylamide precursor asparagine. Acrylamide is formed in potentially harmful concentrations when cereals are treated with high temperatures over a long period during the processing to food products. A promising strategy to reduce the acrylamide formation would be to decrease the precursors in the raw material. The wide range of variation for asparagine content showed that variety selection might have a large influence on the occurrence of acrylamide in the final product. In addition, the moderately high heritability suggested that successful breeding for lower asparagine content is possible. This conclusion is supported by the observation of no strong negative correlations between asparagine content and a number of other important traits. The genome-wide association mapping resulted in the detection of eight putative QTL, which jointly explained 78.5% of the genetic variance. A putative QTL on chromosome 7B explained with, 18.4%, the highest proportion of the genetic variance for a single marker. For spelt wheat, we assessed a high number of quality traits but placed a special emphasis on the flavor and odor of bread produced from 30 different varieties. Interestingly, we observed a significant genetic variation for bread flavor and a heritability estimate of moderate magnitude. This suggests that even for bread flavor a successful selection appears possible. Taken together, for most traits the genome-wide association mapping resulted in the detection of a high number of putative QTL. This indicates a complex genetic architecture, typical for predominantly quantitatively inherited traits. However, few of the putative QTL explained a large proportion of the genetic variance, so that they might have the potential to be used in marker-assisted selection. In order to examine the potential of genomic selection, I performed a five-fold cross validation for the different quality traits. I could confirm previous findings that the integration of QTL information as fixed effects in the genomic prediction model increased the prediction abilities considerably. The average prediction abilities for most traits suggested a high potential for genomic selection in breeding programs. In conclusion or results form a good basis for further research but more importantly already deliver valuable knowledge that can be used as guideline to advance wheat breeding programs for improved quality.
Implementation and optimization of the doubled haploid technology for tropical maize (Zea mays L.) breeding programs
(2012) Prigge, Vanessa; Melchinger, Albrecht E.
Doubled haploid (DH) technology is currently the fastest way to achieve homozygosity in maize and it offers numerous quantitative genetic, operational, and economic advantages. Hybrid maize breeding with DH lines is common in temperate areas, yet adoption of this technology is still to be realized in tropical areas. Therefore, the main goal of my thesis project was to establish and validate the DH technology for tropical maize breeding programs at the International Maize and Wheat Improvement Center (CIMMYT) in Mexico. In vivo production of maternal haploids and DH lines involves four steps: (i) inducing haploidy by pollinating source germplasm with pollen of a haploid inducer; (ii) identifying seeds with haploid embryos based on a visually scorable marker; (iii) duplicating chromosomes of putative haploids by treating the seedlings with a mitotic inhibitor; and (iv) self-pollinating DH plants to multiply their seed. To impart knowledge on each of the above steps, we compiled a detailed protocol and produced a publicly available video which will be very useful for capacity building. Lack of reliable information on the performance of temperate inducers under nontemperate conditions is one reason for the slow adoption of DH technology in tropical maize breeding programs. Therefore, we assessed haploid induction rates (HIR) and agronomic performance of three temperate inducers in tropical lowland environments in Mexico. HIR obtained under tropical conditions were similar to those previously reported from evaluations under temperate conditions, indicating that temperate inducers can be used for initiation of DH breeding programs in the tropics. However, the inducers showed poor pollen production, poor seed set, and strong susceptibility to tropical leaf diseases. Hence, better adapted inducers would be advantageous for large-scale induction of haploidy in tropical DH programs. To develop better adapted haploid inducers, segregating populations were generated from crosses between temperate inducers and eight tropical CIMMYT maize lines (CML) from Mexico and Zimbabwe. Mass selection of individual F2 plants was conducted for visually scorable and highly heritable traits, followed by family-based selection for HIR and agronomic traits. Several tropical inducer candidates (TIC) were identified with HIR of up to 10% and notably improved agronomic performance under tropical lowland conditions. Compared to backcrosses to the inducers, backcrosses to the CML showed similar HIR combined with a significantly later anthesis date and improved plant vigor. Hence, backcrossing to the adapted parent may be a suitable approach to improve adaptation of new inducers while maintaining high HIR levels. Furthermore, we screened randomly chosen South American maize accessions and observed HIR of up to 3%, suggesting that novel sources of haploid induction ability may be present in CIMMYT?s vast germplasm collection. Although extensively exploited in DH line production, the genetic mechanisms underlying in vivo induction of maternal haploids in maize are still largely unknown. We conducted comparative quantitative trait locus (QTL) mapping for HIR to explore the genetic architecture of this phenomenon. Segregating populations were generated from four crosses composed of two temperate haploid inducer lines and three non-inducer lines. One major QTL on chromosome 1 (qhir1; bin 1.04) explaining up to 66% of the genotypic variance was detected in the three populations involving non-inducer lines. Hence, bin 1.04 represents an interesting region for map-based cloning. Further, qhir1 was affected by strong segregation distortion against the inducer allele, indicating that natural selection disfavors haploid induction ability. Seven QTL with smaller effects were detected in the CAUHOI×UH400 population. Further, we proposed a conceptual genetic framework for inheritance of in vivo haploid induction ability in maize. Common methods for artificial duplication of haploid chromosome sets mostly involve toxic and costly reagents and are extremely labor-intensive. This leads to serious bottlenecks during DH line development. When screening haploid populations derived from 260 diverse temperate and tropical source germplasm, we observed significant genetic variation for fertility-related traits, suggesting that haploid fertility can be effectively improved by recurrent selection. This may facilitate abolishment of artificial chromosome doubling during DH production, which seems particularly relevant for enabling small national maize breeding programs and seed companies in developing countries to adopt the DH technology. To study the suitability of different population types for DH line extraction, we developed 131 DH lines from five tropical elite single crosses (SC) and five tropical open-pollinated populations (OP) and evaluated them for testcross performance in Mexico. While testcross grain yield means of the two population types did not differ significantly, significant genetic variance was only revealed for OP-derived DH lines. Several DH lines from OP excelled in testcross performance and may be useful for tropical hybrid breeding programs. In addition, tropical OP may harbor valuable untapped genetic variation that can effectively be exploited with DH technology. This thesis work demonstrated that established protocols for in vivo DH line development can be readily applied to tropical maize breeding programs. Adoption of the DH technology promises to greatly increase the efficiency of breeding programs and DH lines are also an exciting tool to (i) immortalize genetic resources, (ii) conduct high-resolution genetic analyses of important traits, and (iii) accelerate the arrival of improved varieties to farmers? fields.
Physiologische und genetische Einflüsse auf die Qualität von Schweinefleisch aus baden-württembergischen Gebrauchskreuzungen
(2012) Fecke, Anna; Weiler, Ulrike
What genotypes, basing on the genetic lines supplied by German Genetic, guarantees both a high-value carcass and excellent pork quality and high eating quality and also how the criteria of fertility, weight development and yield at slaughter, relate to the criteria of pork quality. 10 genotypes were studied. Therefore the sows crossbred represent typically genotypes in Baden-Württemberg as well as the Leicoma hybrid sows. These sows were bred at the LSZ Boxberg with Pietrain and Duroc boars. The sows of the LW*(LC*DL) had the highest fertility rate. The boar lines showed no influence on either the birth weight or fertility parameters. The boar line, however, did reflect a highly significant influence on the daily gain in all further production periods (Duroc vs. Pietrain: suckling +8%; rearing +3,8%; fattening +6,5%).The offspring from the sows LW*(LC*DL) had the greatest daily gain in the suckling period and had a higher weaning weight (+6%, p<0.05) than the offspring from the LW*(SH*DL), which achieved the lowest overall weaning weight. On analyzing the relationship between the development weights in the various production periods and the birth weight, it was obvious that the birth weight provides a significant positive influence on the performance in every production period, except for rearing. Indeed, in the rearing period the animals with a high birth weight tended to show low daily gains, whereas the piglets with a low birth weight were able to partially compensate for the early growth deficit during this period. The Pietrain offspring had more lean meat content than the Duroc offspring. The dissection in Trial #2 shows that the Pietrain offspring had 3.3% more ham content and 4.0% more of the valuable cuts. The Duroc offspring had less lean meat content in the belly (-4.2%, Gruber Formula), more back fat (+13.7%), more leaf fat (+14.6%), and 12.5% more corrected fat area than the Pietrain offspring. The offspring of the sows LC*LW had a significantly shorter carcass than the offspring of the other sows. The offspring from the 50% Leicoma sows showed the greatest corrected fat area. The offspring from the sows LW*(LC*DL) had 17.1% less corrected fat area. The correlation analysis resulted in the established relationships. Especially of a practical interest, is the close relationship between lean meat content (FOM) and the pork underbelly (Gruber Formula) (r=0.92; n=240; p<0.001). For nearly every parameter the results of the pork quality grading under practical conditions (Trial #1) tended toward improved values for the pigs with Duroc genes, which showed a significantly lower drip loss. The influence of the sows on pork quality parameters was negligible. Besides these parameters, some carcasses were also characterized with PSE qualities (pH1<5.8; conductivity 24hr p.m.>8.0mS/cm). In Trial #1, based on the pH-readings at the slaughterhouse, almost no carcasses (0.15%) were identified with PSE, whereas the conductivity measurements in ham, 5.79% of the carcasses were identified as PSE. In Trial #2, 15.0% of the animals were PSE based on pH1 or conductivity measurements in the loin and ham. There were 5 carcasses which have PSE after both measurements in loin and ham. In the histochemical analysis of the muscle fiber classification the only difference between the boar lines was found in the percentage of red fibers. The eating quality tests revealed an influence from the boar line. In general, all genotypes produced a high quality lean meat content according to the market requirements. As to expectation the improved pork quality of the Duroc breed was justified by the best eating quality, an improved water-holding capacity and a higher intramuscular fat content. An acceptable overall pork quality can be achieved by pairing the offspring from the Pietrain*LW*(LC*DL). The offspring with some Schwäbisch-Hall genes have an opportunity to establish a regional market. However, their performance was not convincing because in fertility, in daily gain, and even in pork quality they attained below average values. Nevertheless, an optimal pork quality can be achieved more efficiently with other genotypes. On establishing predicting criteria, the percentage of PSE of the pork carcasses is quite positive. The superiority of the 24hr p.m. conductivity value for the drip loss predict is evident here. The measurement of the conductivity subsume the effects of slaughtering and cooling and is more appropriate than the pH1 value, especially, for the incoming inspection in the deboning area as well as for quality assurance.
Sorghum breeding strategies for phosphorus-limited environments in Western Africa : from field to genome level
(2014) Leiser, Willmar Lukas; Haussmann, Bettina
A growing world population juxtaposed with dwindling phosphorus (P) resources present new challenges to current and future global agricultural production. The burden of depleting phosphorus resources is particularly felt in sub-Saharan Africa (SSA). The expected doubling of its population by 2050 and the widespread poor soil fertility will pose an enormous task to future food security in SSA. Plant breeding can be considered as one major factor to improve agricultural production under these harsh low-input conditions. Nevertheless, until recently there have been no thorough breeding efforts to enhance crop production for low-P soil conditions in SSA. Sorghum (Sorghum bicolor L. Moench) is the world’s fifth and Africa’s second most grown cereal crop. Sorghum is a staple crop of SSA and is mostly grown in resource poor regions under low-input cropping conditions, with the largest share in West Africa (WA). Its good adaptation to harsh environmental conditions makes it an important crop for the arid and semi-arid regions, hence a crop vital for food security and increasingly farm income in WA. Breeding sorghum specifically targeting P-limited soils is considered as one of the major challenges for future food production and can serve millions of smallholder farmers in WA. Nevertheless, plant breeders are mostly reluctant to conduct breeding experiments under low-input conditions due to a higher spatial variability of soil properties leading to a lower response to selection. In an unprecedented large scale multi-environment experiment from 2006-2012 in three WA countries, namely Mali, Senegal and Niger, 187 WA sorghum genotypes were evaluated for their performance under P-sufficient and P-deficient conditions. The main goal of this study was to establish a breeding strategy for sorghum targeting P-limited environments. In order to establish such a strategy, the following objectives were defined: (I) to evaluate the impact of spatial models on genotypic selection in low-input field trials, (II) to develop a selection strategy for sorghum targeting P-limited environments, based on quantitative genetic parameters and (III) to identify genomic regions influencing sorghum performance in P-limited environments using modern genomic tools. The major findings of this study can be summarized as follows: Spatial models can increase the precision and efficiency especially of low-input field trials and may lead to different genotype rankings. Hence spatial models and/or adequate field designs are necessary tools for efficient genotype selection under low-input conditions and must be considered in a breeding program targeting P-limited conditions. Sorghum performance is severely impeded by low-P soil conditions and shows large grain yield and plant height reductions and delayed flowering. Nevertheless, WA sorghum is generally well adapted to low-P soil conditions and shows a large exploitable genetic variation for P efficiency. Direct selection under low-P conditions is feasible, necessary and more efficient than indirect selection under high-P conditions and should be pursued in a breeding program targeting P-limited environments. Landrace genotypes are more specifically adapted to low-P conditions and show a higher P acquisition capacity, Durra and Guinea race sorghums show a similar specific low-P adaptation, hence these genotype groups are very promising source germplasm for further breeding efforts. Photoperiod sensitive genotypes show less delay in heading, a higher P acquisition rate and a specific low-P adaptation, hence should be considered for climate and low-P resilience breeding. Selection for low P concentration of grain can be used to enhance internal P use efficiency, therefore decreasing further soil P mining. WA sorghum shows a large genetic diversity, hence providing a valuable source for genetic studies examining the underlying genetics of low-P adaptation. There are many genomic regions involved in sorghum adaptation to low-P soil conditions. Nevertheless, some regions could be identified as major contributors, showing large effects on and strong associations to genotypic performance. Molecular markers in sorghum homologs of the major P efficiency gene PSTOL1 from rice stably enhanced P uptake and crop performance through an increased root growth of sorghum under low-P soil conditions and can be used in marker assisted selection for grain yield production under P-limited conditions. Furthermore, it was observed that grain yield production under P-limited conditions and Al-tolerance are pleiotropically regulated by the same genomic region and most probably the same gene SbMATE. Molecular markers of this region and within the gene SbMATE should be used for marker assisted selection to simultaneously enhance the tolerance to two of the most serious abiotic stresses for sorghum in WA, Al toxicity and P deficiency. WA Guinea race sorghums are an excellent source not only for low-P specific alleles, but also for Al-tolerance and represent therefore an excellent source germplasm for allele mining and marker assisted selection. Genomic selection appears to be a very promising approach to further increase the response to selection. But methods giving more weight to single molecular markers linked to Al-tolerance should be considered. The laid out results show that breeding sorghum specifically targeting P-limited conditions is necessary and feasible using advanced statistical models and modern genetic tools, and should be pursued as a major selection criterion in WA sorghum breeding programs. Nevertheless, only by combining agronomic and socio-economic measures with plant breeding efforts, millions of WA smallholder farmers can be reached and major yield increases can be expected in the near future.