Alleles For Traits Research Articles

Abstract 1442: Analysis of cis-eQTLs in normal and tumor-derived pancreatic tissues reveals functional insights, including for the 9q34.1 ABO pancreatic cancer risk locus

Abstract Objective: To elucidate the genetic architecture of gene expression in pancreatic tissues. Design: We performed expression quantitative trait locus (eQTL) and allele specific expression (ASE) analyses using RNA-sequence data and 1000 Genomes (1000G) imputed GWAS genotypes from 95 fresh frozen histologically normal pancreatic tissue samples. Data from 115 pancreatic tumor-derived tissue samples from The Cancer Genome Atlas (TCGA) was included for comparison. Results: We identified 38,615 cis-eQTLs (corresponding to 484 Genes) in histologically normal tissues and 39,713 cis-eQTL (corresponding to 237 Genes) in tumor tissues (FDR<0.1), with the strongest effects seen near transcriptional start sites (TSS). Approximately 23% and 42% of genes with significant cis-eQTLs (eGenes) appeared to be specific for tumor and normal derived tissues, respectively. Significant enrichment of cis-eQTL variants was noted in noncoding regulatory regions marked by modified histones, DNAse hypersensitivity and bound transcription factors, in particular for pancreatic tissues (1.53-3.12 fold, P≤0.0001), indicating tissue-specific functional relevance. A common pancreatic cancer risk locus on 9q34.2 in the ABO gene (rs687289) was associated with ABO expression in histologically normal (P=5.8x10-8) and tumor-derived (P=8.3x10-5) pancreatic tissues. The high linkage disequilibrium (LD) between this variant and the O blood group generating deletion variant in exon 6 of ABO suggested that nonsense-mediated decay (NMD) of the “O” mRNA could explain the eQTL. However, knock-down of crucial NMD regulators did not influence decay of the ABO “O” mRNA, indicating that a gene regulatory element influenced by pancreatic cancer risk alleles may underlie the eQTL. Conclusions: We have identified cis-eQTLs representing potential functional regulatory variants in the pancreas and generated a rich dataset for further studies on gene expression and regulation in pancreatic tissues. Citation Format: Laufey T. Amundadottir, Soren Lykke Andresen, Wenming Xiao, Jason Hoskins, Ashley Jermusyk, Lauren Rost, Irene Collins, Jinping Jia, Michael Mobaraki, Bin Zhu, Robert Kurtz, Hemang Parikh, Lei Song, Meredith Yeager, Torben Jensen, William Bamlet, Nilanjan Chatterjee, Brian Wolpin, Jill Smith, Sara Olson, Gloria Petersen, Jianxin Shi, Mingfeng Zhang. Analysis of cis-eQTLs in normal and tumor-derived pancreatic tissues reveals functional insights, including for the 9q34.1 ABO pancreatic cancer risk locus [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1442. doi:10.1158/1538-7445.AM2017-1442

Investigation of the Genetic Diversity and Quantitative Trait Loci Accounting for Important Agronomic and Seed Quality Traits in Brassica carinata.

Brassica carinata (BBCC) is an allotetraploid in Brassicas with unique alleles for agronomic traits and has huge potential as source for biodiesel production. To investigate the genome-wide molecular diversity, population structure and linkage disequilibrium (LD) pattern in this species, we genotyped a panel of 81 accessions of B. carinata with genotyping by sequencing approach DArTseq, generating a total of 54,510 polymorphic markers. Two subpopulations were exhibited in the B. carinata accessions. The average distance of LD decay (r2 = 0.1) in B subgenome (0.25 Mb) was shorter than that of C subgenome (0.40 Mb). Genome-wide association analysis (GWAS) identified a total of seven markers significantly associated with five seed quality traits in two experiments. To further identify the quantitative trait loci (QTL) for important agronomic and seed quality traits, we phenotyped a doubled haploid (DH) mapping population derived from the “YW” cross between two parents (Y-BcDH64 and W-BcDH76) representing from the two subpopulations. The YW DH population and its parents were grown in three contrasting environments; spring (Hezheng and Xining, China), semi-winter (Wuhan, China), and spring (Wagga Wagga, Australia) across 5 years for QTL mapping. Genetic bases of phenotypic variation in seed yield and its seven related traits, and six seed quality traits were determined. A total of 282 consensus QTL accounting for these traits were identified including nine major QTL for flowering time, oleic acid, linolenic acid, pod number of main inflorescence, and seed weight. Of these, 109 and 134 QTL were specific to spring and semi-winter environment, respectively, while 39 consensus QTL were identified in both contrasting environments. Two QTL identified for linolenic acid (B3) and erucic acid (C7) were validated in the diverse lines used for GWAS. A total of 25 QTL accounting for flowering time, erucic acid, and oleic acid were aligned to the homologous QTL or candidate gene regions in the C genome of B. napus. These results would not only provide insights for genetic improvement of this species, but will also identify useful genetic variation hidden in the Cc subgenome of B. carinata to improve canola cultivars.

Genetic Analysis of Teosinte Alleles for Kernel Composition Traits in Maize.

Teosinte (Zea mays ssp. parviglumis) is the wild ancestor of modern maize (Zea mays ssp. mays). Teosinte contains greater genetic diversity compared with maize inbreds and landraces, but its use is limited by insufficient genetic resources to evaluate its value. A population of teosinte near isogenic lines (NILs) was previously developed to broaden the resources for genetic diversity of maize, and to discover novel alleles for agronomic and domestication traits. The 961 teosinte NILs were developed by backcrossing 10 geographically diverse parviglumis accessions into the B73 (reference genome inbred) background. The NILs were grown in two replications in 2009 and 2010 in Columbia, MO and Aurora, NY, respectively, and near infrared reflectance spectroscopy and nuclear magnetic resonance calibrations were developed and used to rapidly predict total kernel starch, protein, and oil content on a dry matter basis in bulk whole grains of teosinte NILs. Our joint-linkage quantitative trait locus (QTL) mapping analysis identified two starch, three protein, and six oil QTL, which collectively explained 18, 23, and 45% of the total variation, respectively. A range of strong additive allelic effects for kernel starch, protein, and oil content were identified relative to the B73 allele. Our results support our hypothesis that teosinte harbors stronger alleles for kernel composition traits than maize, and that teosinte can be exploited for the improvement of kernel composition traits in modern maize germplasm.

Harnessing Crop Wild Relatives for Crop Improvement

Crop wild relatives (CWRs) are the potential source of novel traits and genetic variation in food crops with narrow genetic base. CWRs include immediate progenitor of crop species and other species of plants which are closer to them in near evolutionary history. CWRs are the sources of novel alleles for several important traits of nutritional and agronomical importance. Introgression of such valuable alleles into working germplasm of a breeding programme depends on sexual compatibility of CWRs with crop species in cultivation. Scientific techniques have been developed to overcome compatibility among them up to certain extent. Simultaneous discovery and transfer of useful alleles into cultivable background have been demonstrated in certain crop species with success. Utilisation of completely incompatible species has been made easier by methods such as somatic hybridization. With ever increasing innovations in the field of genomics science, hope to harness the potential of CWR has grown up to new heights. CWRs have been successfully utilised to enhance quality of crop produce in wheat, barley, tomato, etc., and also have been exploited to create new species such as triticale as well as to understand crop evolutionary history in different crops. CWRs are also a good source of cytoplasmic male sterility which makes them amenable to boost commercial breeding programs. Many CWRs are natural source of abiotic and biotic stresses. Importance of CWR has become more relevant in the era where threat of climate change is apparent and mitigation approaches such as transgenics are being increasingly criticised on many fronts. In the era facing the challenges of genetic erosion of diversity and extinction of species, systematic collection, conservation, and characterization of available genetic diversity of CWRs is immensely important. Prebreeding of wild germplasm is among other challenges for successful utilization of such highly potential genetic resources for enhancing crop breeding efforts.

Identification of molecular markers associated with kernel iron and zinc concentrations in groundnut (Arachis hypogaea L.)

Micronutrient malnutrition affects more than one-half of the world’s population, especially women and pre-school children. Poor consumers in developing countries acquire roughly one-half of their total iron intakes and a higher percentage of zinc intakes from staple foods. Bio-fortification, an approach of breeding crop plants for higher micronutrient concentration, is a cost effective and sustainable solution for tackling the micronutrient deficiencies. Developing countries, where micronutrient deficiencies are widespread, contribute world’s maximum peanut area and production. Thus, peanut can contribute significantly towards reduction of protein-energy and micronutrient malnutrition. With the advent of molecular markers, by using segregating populations for the trait of interest for breeders, it has now become effective to map genes or Quantitative Traits Loci (QTLs) and identify valuable alleles for the corresponding traits. In the present study, an F 2:3 mapping population derived from the cross ICGV 06099 × ICGV 93468 was genotyped using 33 polymorphic SSR markers to identify the putative genomic regions associated with the kernel iron and zinc concentrations in groundnut using Single Marker Analysis (SMA). Results revealed that three markers viz ., SEQ1B09 (0.23 %), IPAHM245 (2.19 %) and SEQ9G05 (6.34 %) showed significant association with the kernel iron and three markers viz., GM2638 (1.75 %), IPAHM245 (2.25 %) and SEQ9G05 (6.01 %) showed significant association with kernel zinc concentration. Significant positive association (0.549) was observed between kernel iron and zinc concentrations. Validation of these markers in an alternate F 2:3 population derived from the cross ICGV 06040 × ICGV 87141 also showed strong association of these markers with the traits of interest.

Marker detection and elite allele mining for yield traits in Upland cotton (Gossypium hirsutum L.) by association mapping

SUMMARYAssociation mapping based on linkage disequilibrium is an effective approach for dissecting the inheritance of complex multi-gene traits. In the present study, association mapping was performed for yield traits based on 172 popular Upland cotton (Gossypium hirsutum L.) cultivars in China and 331 polymorphic simple sequence repeat (SSR) markers. The gene diversity index of 331 markers ranged from 0·0387 to 0·7799 with an average of 0·4002, and the polymorphism information content ranged from 0·0379 to 0·7473 with an average of 0·3375. A total of 93 significantly associated markers for seven yield traits were identified across more than one environment, among which 11 were for seed cotton yield, 12 for lint yield, 11 for boll number per plant, 13 for boll weight, 21 for lint percentage, 14 for lint index and 11 for seed index. The corresponding ranges in phenotypic variation explained by markers across four environments for these seven traits were 1·75–10·49, 1·75–9·34, 2·84–11·80, 2·59–9·89, 2·38–13·97, 2·73–14·82 and 2·50–11·88%, respectively. Some of the yield-associated markers detected were found to be linked to or associated with the same traits identified in previous studies. Furthermore, elite alleles for yield traits were also mined. The present study can provide useful information for further understanding the genetic basis of yield traits, and facilitate high-yield breeding by molecular design in Upland cotton.

Genetic Analysis in Maize Foundation Parents with Mapping Population and Testcross Population: Ye478 Carried More Favorable Alleles and Using QTL Information Could Improve Foundation Parents.

The development of maize foundation parents is an important part of genetics and breeding research, and applying new genetic information to produce foundation parents has been challenging. In this study, we focused on quantitative trait loci (QTLs) and general combining ability (GCA) of Ye478, a widely used foundation parent in China. We developed three sets of populations for QTL mapping and to analyze the GCA for some agronomic traits. The assessment of 15 traits resulted in the detection of 251 QTLs in six tested environments, with 119 QTLs identified through a joint analysis across all environments. Further, analyses revealed that most favorable alleles for plant type-related traits were from Ye478, and more than half of the favorable alleles for yield-related traits were from R08, another foundation parent used in southwestern China, suggesting that different types of foundation parents carried different favorable alleles. We observed that the GCA for most traits (e.g., plant height and 100-kernel weight) was maintained in the inbred lines descended from the foundation parents. Additionally, the continuous improvement in the GCA of the descendants of the foundation parents was consistent with the main trend in maize breeding programs. We identified three significant genomic regions that were highly conserved in three Ye478 descendants, including the stable QTL for plant height. The GCA for the traits in the F7 generation revealed that the QTLs for the given traits per se were affected by additive effects in the same way in different populations.

Decoded Rice Genome for Decipherment of Origin, Domestication and Functional Attributes of Rice

Rice is inseparable part of Indian culture and life. It is also a staple not only for India but for major world population, especially in developing nations. Out of about 450 million tons of milled rice produced world-wide in 2015, more than 100 million tons has been produced in India. The sequence of its 12 chromosomes was decoded under the auspices of an International Rice Genome Sequencing Project (IRGSP), involving ten nations including India. Indian Initiative on Rice Genome Sequencing (IIRGS) supported by the Government of India related to chromosome 11 and was the first Indian effort on high-throughput genome-wide sequencing. The present day rice genome of about 400 Mb has resulted from whole genome, segmental and tandem duplications. Non-shattering seeds and white seed are some of the traits distinguishing domesticated from wild rice. Interestingly, these traits are due to the presence of certain alleles most likely selected by human beings long ago. Rice cultivation possibly began in South-central China near Yangtze river several thousands years ago. Other evidences suggest Ganges river valley as origin of rice cultivation. Some genetic evidences also suggest possibility of hybridization between Japonica and native wild rice. While global occurrence of certain alleles for domestication traits (shattering and pericarp colour) reflects on single domestication event, recent genome-wide analysis indicates multiple domestication events. Decoded rice genome has served as an invaluable resource for structural and functional annotation of about 32,000 genes in rice and, so far, function of over 2,000 genes has been unraveled by forward and reverse genetics approaches. By deploying, microarray-based transcriptome profiling, over-expression and knock-down transgenics, association and molecular mapping, and haplotyping approaches, we have defined evolution, phylogenetic relationship and composition of over 25 gene families along with biological function of several selected genes and regulatory elements related to seed development, male-sterility, hybrid vigour and stress tolerance. This is expected to help genetic enhancement of rice. The Rice Genome representation included here is prepared by Dr. S. Parida, NIPGR. * National Institute of Plant Genome Research, New Delhi 110067; Email: akhilesh@genomeindia.org Indian Journal of History of Science, 51.2.2 (2016) 354 DOI: 10.16943/ijhs/2016/v51i2.2/48448 DECODING RICE GENOME

Germplasm Architecture Revealed through Chromosomal Effects for Quantitative Traits in Maize.

Germplasm architecture refers to how favorable alleles for a given trait are distributed across the genome in a germplasm collection. Our objective was to assess germplasm architecture for quantitative traits among US maize ( L.) inbreds. A total of 271 inbreds were genotyped at 28,626 single nucleotide polymorphism (SNP) loci and phenotyped for anthesis date, plant height, starch and protein concentration, and resistance to northern corn leaf blight (NCLB, caused by ). Chromosomal effects were calculated as the sum of the trait effects of SNP alleles carried on a specific chromosome by an inbred. The chromosomal effects were further decomposed into the mean effects of chromosomes, mean effects of inbreds, and chromosome × inbred effects. On average, none of the 10 maize chromosomes was particularly rich or poor in favorable quantitative trait locus (QTL) alleles. However, extreme values of chromosome × inbred effects often involved chromosomes 5 and 8 for anthesis date, chromosomes 1 and 5 for plant height, and chromosome 9 for protein concentration. Inbreds with one or two chromosomes deficient in favorable alleles were candidates for improvement via chromosome-substitution lines. Specific chromosomes for which each of five genetic backgrounds (B73, Mo17, Oh43, A321, and PH207) were rich or poor for unknown favorable alleles were also identified. Chromosomal effects varied widely even when prior association mapping in the same germplasm collection had failed to identify any QTL. Genomewide marker effects, particularly when partitioned into chromosomal effects, provide a simple way to dissect germplasm architecture for quantitative traits.

Genetic Diversity and Elite Allele Mining for Grain Traits in Rice (Oryza sativa L.) by Association Mapping.

Mining elite alleles for grain size and weight is of importance for the improvement of cultivated rice and selection for market demand. In this study, association mapping for grain traits was performed on a selected sample of 628 rice cultivars using 262 SSRs. Grain traits were evaluated by grain length (GL), grain width (GW), grain thickness (GT), grain length to width ratio (GL/GW), and 1000-grain weight (TGW) in 2013 and 2014. Our result showed abundant phenotypic and genetic diversities found in the studied population. In total, 2953 alleles were detected with an average of 11.3 alleles per locus. The population was divided into seven subpopulations and the levels of linkage disequilibrium (LD) ranged from 34 to 84 cM. Genome-wide association mapping detected 10 marker trait association (MTAs) loci for GL, 1MTAs locus for GW, 7 MTAs loci for GT, 3 MTAs loci for GL/GW, and 1 MTAs locus for TGW. Twenty-nine, 2, 10, 5, and 3 elite alleles were found for the GL, GW, GT, GL/GW, and TGW, respectively. Optimal cross designs were predicted for improving the target traits. The accessions containing elite alleles for grain traits mined in this study could be used for breeding rice cultivars and cloning the candidate genes.

A method to decipher pleiotropy by detecting underlying heterogeneity driven by hidden subgroups applied to autoimmune and neuropsychiatric diseases.

There is growing evidence of shared risk alleles between complex traits (pleiotropy), including autoimmune and neuropsychiatric diseases. This might be due to sharing between all individuals (whole-group pleiotropy), or a subset of individuals within a genetically heterogeneous cohort (subgroup heterogeneity). BUHMBOX is a well-powered statistic distinguishing between these two situations using genotype data. We observed a shared genetic basis between 11 autoimmune diseases and type 1 diabetes (T1D, p<10−4), and 11 autoimmune diseases and rheumatoid arthritis (RA, p<10−3). This sharing was not explained by subgroup heterogeneity (corrected pBUHMBOX>0.2, 6,670 T1D cases and 7,279 RA cases). Genetic sharing between seronegative and seropostive RA (p<10−9) had significant evidence of subgroup heterogeneity, suggesting a subgroup of seropositive-like cases within seronegative cases (pBUHMBOX=0.008, 2,406 seronegative RA cases). We also observed a shared genetic basis between major depressive disorder (MDD) and schizophrenia (p<10−4) that was not explained by subgroup heterogeneity (pBUHMBOX=0.28 in 9,238 MDD cases).

A high density genetic map and QTL for agronomic and yield traits in Foxtail millet [Setaria italica (L.) P. Beauv

BackgroundFoxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China, has been adopted as a model crop for studying C-4 photosynthesis, stress biology and biofuel traits. Construction of a high density genetic map and identification of stable quantitative trait loci (QTL) lay the foundation for marker-assisted selection for agronomic traits and yield improvement.ResultA total of 10598 SSR markers were developed according to the reference genome sequence of foxtail millet cultivar ‘Yugu1’. A total of 1013 SSR markers showing polymorphism between Yugu1 and Longgu7 were used to genotype 167 individuals from a Yugu1 × Longgu7 F2 population, and a high density genetic map was constructed. The genetic map contained 1035 loci and spanned 1318.8 cM with an average distance of 1.27 cM between adjacent markers. Based on agronomic and yield traits identified in 2 years, 29 QTL were identified for 11 traits with combined analysis and single environment analysis. These QTL explained from 7.0 to 14.3 % of phenotypic variation. Favorable QTL alleles for peduncle length originated from Longgu7 whereas favorable alleles for the other traits originated from Yugu1 except for qLMS6.1.ConclusionsNew SSR markers, a high density genetic map and QTL identified for agronomic and yield traits lay the ground work for functional gene mapping, map-based cloning and marker-assisted selection in foxtail millet.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2628-z) contains supplementary material, which is available to authorized users.

Association Analysis of Stem Solidness and Wheat Stem Sawfly Resistance in a Panel of North American Spring Wheat Germplasm

ABSTRACTThe expanding geographical range of wheat stem sawfly (WSS) damage, coupled with the limited number of effective control measures, calls for a need to better characterize and explore the genetic variability for resistance in wheat (Triticum aestivum L.) germplasm from North America. An association‐mapping analysis for stem solidness and wheat stem sawfly resistance was conducted using a set of 244 elite spring wheat lines from 10 North American breeding programs. Three previously identified quantitative trait loci (QTL) for resistance were confirmed, including QTL for stem solidness, heading date, and stem cutting. Three new QTL on chromosomes 2A, 3A, and 5B were identified to be associated with larval mortality and a QTL associated with early stem solidness was identified on chromosome 5D. Genetic variation for late stem solidness is mainly determined by the solid‐stem QTL on chromosome 3B, while variation for early solidness is affected by chromosomal regions on 1B, 3B, and 5D. Potential sources of a novel resistance mechanism causing larval mortality were identified among the panel lines. Favorable alleles for stem solidness and other resistance traits are available within North American wheat germplasm, but only Montana and South Dakota breeding programs appear to have favorable alleles for all QTLs detected in this study. Improvements in wheat stem sawfly management, for both historically impacted areas and for regions first experiencing damage, may be obtained using alleles that already exist in elite germplasm.

Combining ability and heterosis of relevant fruit traits of tomato genotypes for industrial processing

The objective was to estimate the combining ability of lines and heterosis in industrial tomato genotypes for the identification of those with good potential for breeding programs. Ten lines of industrial tomato, 45 hybrids derived from a complete diallel and two commercial check cultivars were evaluated. The combining ability of tomato lines and heterosis of hybrid combinations for fruit-quality related traits were estimated. Non-additive effects predominated in the genetic control of all traits. The parent lines RVTD-04, RVTD-10 and RVTD-08 had an exceptionally high presence of favorable alleles for most traits. High genetic divergence between the parents was observed, contributing positively to significant heterosis values. The above lines can be used in breeding programs to develop tomato hybrids with high performance for characteristics related to industrial processing.

Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits.

We investigated the nuclear simple sequence repeat (SSR) genotypes of 532 rice (Oryza sativa L.) accessions collected from East and Southeast Asia and detected abundant genetic diversity within the population. We identified 6 subpopulations and found a tendency towards directional evolution in O. sativa from low to high latitudes, with levels of linkage disequilibrium (LD) in the 6 subpopulations ranging from 10 to 30 cM. We then investigated the phenotypic data for grain length, grain width, grain thickness and 1,000-grain weight over 4 years. Using a genome-wide association analysis, we identified 17 marker-trait associations involving 14 SSR markers on 12 chromosome arms, and 8 of the 17 associations were novel. The elite alleles were mined based on the phenotypic effects of the detected quantitative trait loci (QTLs). These elite alleles could be used to improve target traits through optimal cross designs, with the expected results obtained by pyramiding or substituting the elite alleles per QTL (independent of possible epistatic effects). Together, these results provide an in-depth understanding of the genetic diversity pattern among rice-grain traits across a broad geographic scale, which has potential use in future research work, including studies related to germplasm conservation and molecular breeding by design.

New QTL alleles for quality-related traits in spring wheat revealed by RIL population derived from supernumerary × non-supernumerary spikelet genotypes.

A population developed from an exotic line with supernumerary spikelets was genetically dissected for eight quality traits, discovering new genes/alleles with potential use in wheat breeding programs. Identifying new QTLs and alleles in exotic germplasm is paramount for further improvement of quality traits in wheat. In the present study, an RIL population developed from a cross of an elite wheat line (WCB414) and an exotic genotype with supernumerary spikelets (SS) was used to identify QTLs and new alleles for eight quality traits. Composite interval mapping for 1,000 kernels weight (TKW), kernel volume weight (KVW), grain protein content (GPC), percent of flour extraction (FE) and four mixograph-related traits identified a total of 69 QTLs including 19 stable QTLs. These QTLs were located on 18 different chromosomes (except 4D, 5D, and 6D). Thirteen of these QTLs explained more than 15% of phenotypic variation (PV) and were considered as major QTLs. In this study, we identified 11 QTLs for TKW (R (2) = 7.2-17.1 %), 10 for KVW (R (2) = 6.7-22.5%), 11 for GPC (R (2) = 4.7-16.9%), 6 for FE (R (2) = 4.8-19%) and 31 for mixograph-related traits (R (2) = 3.2-41.2%). In this population, several previously identified QTLs for SS, nine spike-related and ten agronomic traits were co-located with the quality QTLs, suggesting pleiotropic effects or close linkage among loci. The traits GPC and mixogram-related traits were positively correlated with SS. Indeed, several loci for quality traits were co-located with QTL for SS. The exotic parent contributed positive alleles that increased PV of the traits at 56% of loci demonstrating the suitability of germplasm with SS to improve quality traits in wheat.

Mapping quantitative trait loci determining seed longevity in tobacco (Nicotiana tabacum L.)

Seed longevity is a crucial issue for germplasm conservation and seed marketing. This trait is determined not only by environmental conditions, but also by genetic factors. Molecular mapping of responsible loci has been performed with several crops, but not with tobacco (Nicotianatabacum L.). In the present study, we investigate 122 recombinant inbred lines derived from a cross between the cultivars Florida 301 and Hicks. Four germination-related traits were studied by examining seeds either untreated or after controlled deterioration (CD): total germination (TG, %), normal germination (%), time to reach 50 % of TG (h), and the area under the curve after 200 h of germination. Whereas Hicks exhibited high germination percentage and speed in untreated (fresh) seeds, Florida 301 seems to withstand the CD treatment better, having increased seed longevity. In total, four genomic regions located on four different linkage groups (LGs) were identified to be associated with the selected traits. Positive alleles for the individual traits were contributed by both parents. A major quantitative trait locus (QTL) for high percentage TG located on LG 8/18 appeared in both control and deteriorated seeds and was contributed by Hicks. In contrast, Florida 301 donated a favorable allele for germination speed on LG seven after CD only. The position of this locus compared well with a QTL detected in the same population, in a former study examining resistance against the black shank disease caused by Phytophthora nicotianae). The effects of environmental growing conditions of the mother plants on seed longevity are discussed.

F1 hybrids of BALB/c and C57BL/6 mouse strains respond differently to low-dose ionizing radiation exposure.

There are evidences to show that response to ionizing radiations have genetic influence. To investigate this further, reciprocal F1 hybrids were generated by crossbreeding the radiation-susceptible BALB/c mouse strain with resistant C57BL/6 in a sex-specific manner (BALB/c♂ x C57BL/6♀ = B6BcF1; C57BL/6♂ x BALB/c♂ =BcB6F1). These hybrids were compared with each other and to the parental strains with respect to transcriptional responses to low-dose ionizing radiation exposure (LDIR). The two F1 hybrids showed drastic differences in their gene expression profiles to ionizing radiation exposure particularly in case of the genes involved in DNA damage response and repair process. Also, the inheritance pattern of the gene expression was found to be complex and could not be explained solely on the basis of parental expression pattern. It was concluded that there is a differential transmission of susceptible trait alleles from the parents to F1 progeny which is dependent on the sex of the parent mouse strain used to set up the crosses and other environmental factors.

The Effect of Linkage on Genetic Variances within Biparental Simulated and Zea mays Populations

ABSTRACTHybrid yield improvement in maize (Zea mays L.) has been attributed in part to the development of elite inbred lines within distinct germplasm groups adapted to distinct environments. Breeding largely within groups has caused the accumulation of distinct favorable alleles for adaptation, yield, and yield component traits. Favorable alleles may be linked to other favorable alleles in coupling phase or linked to unfavorable alleles in repulsion phase. To investigate the effects of linkage on genetic variances, we used a simple, two‐locus model to simulate populations of intermated and standard recombinant inbred lines (RILs) derived from parental lines with coupling or repulsion phase loci. Genetic variances differ between simulated intermated RILs (IRIL) and RIL testcross populations as a function of population size, the effect sizes of linked loci, and the genetic distance between loci. We also generated RIL and IRIL testcross (TC) populations from two short‐season inbred lines from different heterotic groups and evaluated yield, three yield component traits, and five flowering time–associated traits. For all nine traits, the inbred lines have accumulated distinct favorable alleles. Genetic variances are high and transgressive phenotypes are frequent in both testcross populations. Intermating does not increase genetic variation. Genetic variances of six traits within the RIL‐TC population are nominally between 1.25 and 1.75‐fold greater than variances within the IRIL‐TC population. We conclude that the genomes of the parental inbred lines may harbor coupling rather than repulsion phase loci and heterosis is unlikely due to pseudo‐overdominance.

Wild barley introgression lines revealed novel QTL alleles for root and related shoot traits in the cultivated barley (Hordeum vulgare L.).

BackgroundRoot is the prime organ that sucks water and nutrients from deep layer of soil. Wild barley diversity exhibits remarkable variation in root system architecture that seems crucial in its adaptation to abiotic stresses like drought. In the present study, we performed quantitative trait locus (QTL) mapping of root and related shoot traits under control and drought conditions using a population of wild barley introgression lines (ILs). This population (S42IL) comprising of genome-wide introgressions of wild barley accession ISR42-8 in the cultivar Scarlett background. Here, we aimed to detect novel QTL alleles for improved root and related shoot features and to introduce them in modern cultivars.ResultsThe cultivar Scarlett and wild barley accession ISR42-8 revealed significant variation of root and related shoot traits. ISR42-8 showed a higher performance in root system attributes like root dry weight (RDW), root volume (RV), root length (RL) and tiller number per plant (TIL) than Scarlett. Whereas, Scarlett exhibited erect type growth habit (GH) as compared to spreading growth habit in ISR42-8. The S42IL population revealed significant and wide range of variation for the investigated traits. Strong positive correlations were found among the root related traits whereas GH revealed negative correlation with root and shoot traits. The trait-wise comparison of phenotypic data with the ILs genetic map revealed six, eight, five, five and four QTL for RL, RDW, RV, TIL and GH, respectively. These QTL were linked to one or several traits simultaneously and localized to 15 regions across all chromosomes. Among these, beneficial QTL alleles of wild origin for RL, RDW, RV, TIL and GH, have been fixed in the cultivar Scarlett background.ConclusionsThe present study revealed 15 chromosomal regions where the exotic QTL alleles showed improvement for root and related shoot traits. These data suggest that wild barley accession ISR42-8 bears alleles different from those of Scarlett. Hence, the utility of genome-wide wild barley introgression lines is desirable to test the performance of individual exotic alleles in the elite gene pool as well as to transfer them in the cultivated germplasm.