scholarly journals Genetic architecture underlying the expression of eight α-amylase trypsin inhibitors

2021 ◽  
Author(s):  
Khaoula EL Hassouni ◽  
Malte Sielaff ◽  
Valentina Curella ◽  
Manjusha Neerukonda ◽  
Willmar Leiser ◽  
...  
Keyword(s):  
Genetic Architecture ◽  
Intestinal Inflammation ◽  
Wheat Breeding ◽  
Trypsin Inhibitors ◽  
Potential Candidate ◽  
Lipid Transfer ◽  
Wheat Cultivars ◽  
Genome Wide ◽  
Close Physical Proximity ◽  
Major Qtl

Abstract Key message Wheat cultivars largely differ in the content and composition of ATI proteins, but heritability was quite low for six out of eight ATIs. The genetic architecture of ATI proteins is built up of few major and numerous small effect QTL. Abstract Amylase trypsin inhibitors (ATIs) are important allergens in baker’s asthma and suspected triggers of non-celiac wheat sensitivity (NCWS) inducing intestinal and extra-intestinal inflammation. As studies on the expression and genetic architecture of ATI proteins in wheat are lacking, we evaluated 149 European old and modern bread wheat cultivars grown at three different field locations for their content of eight ATI proteins. Large differences in the content and composition of ATIs in the different cultivars were identified ranging from 3.76 pmol for ATI CM2 to 80.4 pmol for ATI 0.19, with up to 2.5-fold variation in CM-type and up to sixfold variation in mono/dimeric ATIs. Generally, heritability estimates were low except for ATI 0.28 and ATI CM2. ATI protein content showed a low correlation with quality traits commonly analyzed in wheat breeding. Similarly, no trends were found regarding ATI content in wheat cultivars originating from numerous countries and decades of breeding history. Genome-wide association mapping revealed a complex genetic architecture built of many small, few medium and two major quantitative trait loci (QTL). The major QTL were located on chromosomes 3B for ATI 0.19-like and 6B for ATI 0.28, explaining 70.6 and 68.7% of the genotypic variance, respectively. Within close physical proximity to the medium and major QTL, we identified eight potential candidate genes on the wheat reference genome encoding structurally related lipid transfer proteins. Consequently, selection and breeding of wheat cultivars with low ATI protein amounts appear difficult requiring other strategies to reduce ATI content in wheat products.

Genome-Wide Association Studies (GWAS) for Traits Related to Fodder Quality and Biofuel in Sorghum: Progress and Prospects

2021 ◽  
Vol 28 ◽  
Author(s):  
Vinutha Kanuganahalli Somegowda ◽  
Laavanya Rayaprolu ◽  
Abhishek Rathore ◽  
Santosh Pandurang Deshpande ◽  
Rajeev Gupta
Keyword(s):  
Genetic Architecture ◽  
Association Studies ◽  
Current Status ◽  
Genome Wide Association Studies ◽  
Potential Candidate ◽  
Crop Species ◽  
Fodder Quality ◽  
Genome Wide ◽  
Genomic Regions ◽  
Model Crop

: The main focus of this review is to discuss the current status of the use of GWAS for fodder quality and biofuel owing to its similarity of traits. Sorghum is a potential multipurpose crop, popularly cultivated for various uses as food, feed fodder, and biomass for ethanol. Production of a huge quantity of biomass and genetic variation for complex sugars are the main motivation not only to use sorghum as fodder for livestock nutritionists but also a potential candidate for biofuel generation. Few studies have been reported on the knowledge transfer that can be used from the development of biofuel technologies to complement improved fodder quality and vice versa. With recent advances in genotyping technologies, GWAS became one of the primary tools used to identify the genes/genomic regions associated with the phenotype. These modern tools and technologies accelerate the genomic assisted breeding process to enhance the rate of genetic gains. Hence, this mini-review focuses on GWAS studies on genetic architecture and dissection of traits underpinning fodder quality and biofuel traits and their limited comparison with other related model crop species.

scholarly journals Genetic Basis of Gluten Aggregation Properties in Wheat (Triticum aestivum L.) Dissected by QTL Mapping of GlutoPeak Parameters

2021 ◽  
Vol 11 ◽  
Author(s):  
Zhengfu Zhou ◽  
Ziwei Zhang ◽  
Lihua Jia ◽  
Hongxia Qiu ◽  
Huiyue Guan ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Genetic Basis ◽  
Triticum Aestivum L ◽  
Interval Mapping ◽  
Wheat Breeding ◽  
Human Consumption ◽  
Processing Quality ◽  
Genome Wide ◽  
The Difference ◽  
Major Qtl

Bread wheat is one of the most important crops worldwide, supplying approximately one-fifth of the daily protein and the calories for human consumption. Gluten aggregation properties play important roles in determining the processing quality of wheat (Triticum aestivum L.) products. Nevertheless, the genetic basis of gluten aggregation properties has not been reported so far. In this study, a recombinant inbred line (RIL) population derived from the cross between Luozhen No. 1 and Zhengyumai 9987 was used to identify quantitative trait loci (QTL) underlying gluten aggregation properties with GlutoPeak parameters. A linkage map was constructed based on 8,518 SNPs genotyped by specific length amplified fragment sequencing (SLAF-seq). A total of 33 additive QTLs on 14 chromosomes were detected by genome-wide composite interval mapping (GCIM), four of which accounted for more than 10% of the phenotypic variation across three environments. Two major QTL clusters were identified on chromosomes 1DS and 1DL. A premature termination of codon (PTC) mutation in the candidate gene (TraesCS1D02G009900) of the QTL cluster on 1DS was detected between Luozhen No. 1 and Zhengyumai 9987, which might be responsible for the difference in gluten aggregation properties between the two varieties. Subsequently, two KASP markers were designed based on SNPs in stringent linkage with the two major QTL clusters. Results of this study provide new insights into the genetic architecture of gluten aggregation properties in wheat, which are helpful for future improvement of the processing quality in wheat breeding.

scholarly journals Identification of Genetic Loci of Black Point in Chinese Common Wheat by Genome-Wide Association Study and Linkage Mapping

Plant Disease ◽  
2020 ◽  
Vol 104 (7) ◽  
pp. 2005-2013 ◽  
Author(s):  
Guoguo Lv ◽  
Zhongdong Dong ◽  
Yudan Wang ◽  
Junyou Geng ◽  
Jia Li ◽  
...  
Keyword(s):  
Association Study ◽  
Linkage Mapping ◽  
Genome Wide Association Study ◽  
Wheat Breeding ◽  
Genome Wide Association ◽  
Common Disease ◽  
Wheat Cultivars ◽  
Black Point ◽  
Genome Wide ◽  
A Genome

Black point is a common disease in wheat all over the world. The disease could downgrade wheat quality and cause human health problems. In this study, 406 wheat cultivars were used to investigate black point resistance. In the field tests, 20, 65.5, and 14.5% of the tested cultivars were resistant, moderately resistant, and susceptible, respectively, suggesting that improving black point resistance is necessary in Chinese wheat breeding. A genome-wide association study (GWAS) identified 386 single-nucleotide polymorphisms (SNPs) significantly related to black point resistance in the tested wheat cultivars, and they were located on all chromosomes. Linkage mapping in a biparental population identified three quantitative trait loci (QTL) for black point resistance—QBP.hau-3A, QBP.hau-6D, and QBP.hau-7D—with 6.76, 7.79, and 8.84% phenotypic variation explained, respectively. Based on both the GWAS and linkage analyses, QBP.hau-6D covered six significant SNPs from the GWAS, and the position of these SNPs indicated that this QTL is a new locus for black point resistance. This study provides valuable germplasm for breeding wheat cultivars with resistance to black point and information for further understanding of molecular and genetic basis of black point resistance.

scholarly journals Genome-Wide Association Study Identifies Candidate Genes Related to the Linoleic Acid Content in Soybean Seeds

2021 ◽  
Vol 23 (1) ◽  
pp. 454
Author(s):  
Qin Di ◽  
Angela Piersanti ◽  
Qi Zhang ◽  
Cristina Miceli ◽  
Hui Li ◽  
...  
Keyword(s):  
Linoleic Acid ◽  
Association Study ◽  
Candidate Genes ◽  
Acid Content ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Soybean Seeds ◽  
Potential Candidate ◽  
Genome Wide

Soybean (Glycine max (L.) Merrill) oil is a complex mixture of five fatty acids (palmitic, stearic, oleic, linoleic, and linolenic). The high content of linoleic acid (LA) contributes to the oil having poor oxidative stability. Therefore, soybean seed with a lower LA content is desirable. To investigate the genetic architecture of LA, we performed a genome-wide association study (GWAS) using 510 soybean cultivars collected from China. The phenotypic identification results showed that the content of LA varied from 36.22% to 72.18%. The GWAS analysis showed that there were 37 genes related to oleic acid content, with a contribution rate of 7%. The candidate gene Glyma.04G116500.1 (GmWRI14) on chromosome 4 was detected in three consecutive years. The GmWRI14 showed a negative correlation with the LA content and the correlation coefficient was −0.912. To test whether GmWRI14 can lead to a lower LA content in soybean, we introduced GmWRI14 into the soybean genome. Matrix-assisted laser desorption/ionization time-of-flight imaging mass spectrometry (MALDI-TOF IMS) showed that the overexpression of GmWRI14 leads to a lower LA content in soybean seeds. Meanwhile, RNA-seq verified that GmWRI14-overexpressed soybean lines showed a lower accumulation of GmFAD2-1A and GmFAD2-1B than control lines. Our results indicate that the down-regulation of the FAD2 gene triggered by the transcription factor GmWRI14 is the underlying mechanism reducing the LA level of seed. Our results provide novel insights into the genetic architecture of LA and pinpoint potential candidate genes for further in-depth studies.

scholarly journals Genome-Wide Association Study Uncover the Genetic Architecture of Salt Tolerance-Related Traits in Common Wheat (Triticum aestivum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaoyan Quan ◽  
Jindong Liu ◽  
Ning Zhang ◽  
Chunjuan Xie ◽  
Hongmei Li ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Transmembrane Protein ◽  
Wheat Yield ◽  
Wheat Breeding ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Genome Wide

Soil salinity is a serious threat to wheat yield affecting sustainable agriculture. Although salt tolerance is important for plant establishment at seedling stage, its genetic architecture remains unclear. In the present study, we have evaluated eight salt tolerance–related traits at seedling stage and identified the loci for salt tolerance by genome-wide association study (GWAS). This GWAS panel comprised 317 accessions and was genotyped with the wheat 90 K single-nucleotide polymorphism (SNP) chip. In total, 37 SNPs located at 16 unique loci were identified, and each explained 6.3 to 18.6% of the phenotypic variations. Among these, six loci were overlapped with previously reported genes or quantitative trait loci, whereas the other 10 were novel. Besides, nine loci were detected for two or more traits, indicating that the salt-tolerance genetic architecture is complex. Furthermore, five candidate genes were identified for salt tolerance–related traits, including kinase family protein, E3 ubiquitin-protein ligase-like protein, and transmembrane protein. SNPs identified in this study and the accessions with more favorable alleles could further enhance salt tolerance in wheat breeding. Our results are useful for uncovering the genetic mechanism of salt tolerance in wheat at seeding stage.

Molecular characterization of QTL-allele system for drought tolerance at seedling stage and optimal genotype design using multi-locus multi-allele genome-wide association analysis in a half-sib population of soybean [Glycine max (L.) Merr.]

2020 ◽  
pp. 1-12
Author(s):  
Mueen Alam Khan ◽  
Fei Tong ◽  
Wubin Wang ◽  
Jianbo He ◽  
Tuanjie Zhao ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Association Analysis ◽  
Genetic Architecture ◽  
Weighted Average ◽  
Genome Wide Association ◽  
Sand Culture ◽  
Phenotypic Variance ◽  
Potential Candidate ◽  
Genome Wide Association Analysis ◽  
Genome Wide

Abstract Characterizing the whole genetic architecture of drought tolerance (DT) is a persistent challenge for the breeders. Here we developed a half-sib population comprising of 404 lines of two recombinant inbred line (RIL) populations with M8206 as the joint parent (M8206 × TongShan and ZhengYang × M8206) and tested for its DT under sand culture. The population was sequenced using restriction-site-associated DNA sequencing filtered with minor allele frequency ≥0.01; 55,936 single nucleotide polymorphisms (SNPs) were obtained and assembled into 6137 SNPLDBs (SNP linkage disequilibrium blocks). The restricted two-stage multi-locus genome-wide association analysis characterized with error and false-positive control identified 40 QTLs with 93 alleles on an average of 34.75% of the phenotypic variance (PV) collectively for relative root length (RRL) and relative shoot length (RSL) that served as potential DT indicators. Among these, eight loci corresponded to previously reported QTLs, whereas 32 loci were therefore novel. The identified QTLs with their corresponding alleles for RRL and RSL were organized into QTL-allele matrices, depicting the comprehensive DT genetic architecture of the three parents/half-sib population. From the matrices, we predicted the possible best/optimal genotype with weighted average value (WAV) 1.553 over two indicators, while for the top 10 single crosses among RILs with 95th percentile WAV was 1.218–1.257, transgressive over the parents (0.693–0.794) yet much less than 1.553. From the detected QTL-allele system, 65 potential candidate genes collectively for both indicators explaining on an average of 24.41% PV were annotated and χ2-tested as a DT candidate gene system involving nine biological processes.

scholarly journals The Genetic Architecture of Grain Yield in Spring Wheat Based on Genome-Wide Association Study

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuyao Li ◽  
Jingquan Tang ◽  
Wenlin Liu ◽  
Wenyi Yan ◽  
Yan Sun ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Spring Wheat ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Wheat Breeding ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

Uncovering the genetic architecture for grain yield (GY)–related traits is important for wheat breeding. To detect stable loci for GY-related traits, a genome-wide association study (GWAS) was conducted in a diverse panel, which included 251 elite spring wheat accessions mainly from the Northeast of China. In total, 52,503 single nucleotide polymorphisms (SNPs) from the wheat 55 K SNP arrays were used. Thirty-eight loci for GY-related traits were detected and each explained 6.5–16.7% of the phenotypic variations among which 12 are at similar locations with the known genes or quantitative trait loci and 26 are likely to be new. Furthermore, six genes possibly involved in cell division, signal transduction, and plant development are candidate genes for GY-related traits. This study provides new insights into the genetic architecture of GY and the significantly associated SNPs and accessions with a larger number of favorable alleles could be used to further enhance GY in breeding.

scholarly journals A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shenping Zhou ◽  
Rongrong Ding ◽  
Fanming Meng ◽  
Xingwang Wang ◽  
Zhanwei Zhuang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Growth And Development ◽  
Genetic Architecture ◽  
Association Studies ◽  
Meta Analysis ◽  
Average Daily Gain ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Daily Gain

Abstract Background Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. Results In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. Conclusions We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

scholarly journals Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Raju Bheemanahalli ◽  
Montana Knight ◽  
Cherryl Quinones ◽  
Colleen J. Doherty ◽  
S. V. Krishna Jagadish
Keyword(s):  
Grain Size ◽  
Candidate Genes ◽  
Gene Network ◽  
Genome Wide Association ◽  
Potential Candidate ◽  
Genetic Loci ◽  
Stay Green ◽  
Yield And Quality ◽  
Genome Wide ◽  
Wide Range

AbstractHigh night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.

scholarly journals Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture

2016 ◽  
Vol 283 (1835) ◽  
pp. 20160569 ◽  
Author(s):  
M. E. Goddard ◽  
K. E. Kemper ◽  
I. M. MacLeod ◽  
A. J. Chamberlain ◽  
B. J. Hayes
Keyword(s):  
Complex Traits ◽  
Genetic Architecture ◽  
Quantitative Traits ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Crop Breeding ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Phenotype Identification

Complex or quantitative traits are important in medicine, agriculture and evolution, yet, until recently, few of the polymorphisms that cause variation in these traits were known. Genome-wide association studies (GWAS), based on the ability to assay thousands of single nucleotide polymorphisms (SNPs), have revolutionized our understanding of the genetics of complex traits. We advocate the analysis of GWAS data by a statistical method that fits all SNP effects simultaneously, assuming that these effects are drawn from a prior distribution. We illustrate how this method can be used to predict future phenotypes, to map and identify the causal mutations, and to study the genetic architecture of complex traits. The genetic architecture of complex traits is even more complex than previously thought: in almost every trait studied there are thousands of polymorphisms that explain genetic variation. Methods of predicting future phenotypes, collectively known as genomic selection or genomic prediction, have been widely adopted in livestock and crop breeding, leading to increased rates of genetic improvement.

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