The Genetic Architecture of Milling Quality in Spring Oat Lines of the Collaborative Oat Research Enterprise

Most oat grains destined for human consumption must possess the ability to pass through an industrial de-hulling process with minimal breakage and waste. Uniform grain size and a high groat to hull ratio are desirable traits related to milling performance. The purpose of this study was to characterize the genetic architecture of traits related to milling quality by identifying quantitative trait loci (QTL) contributing to variation among a diverse collection of elite and foundational spring oat lines important to North American oat breeding programs. A total of 501 lines from the Collaborative Oat Research Enterprise (CORE) panel were evaluated for genome-wide association with 6 key milling traits. Traits were evaluated in 13 location years. Associations for 36,315 markers were evaluated for trait means across and within location years, as well as trait variance across location years, which was used to assess trait stability. Fifty-seven QTL influencing one or more of the milling quality related traits were identified, with fourteen QTL mapped influencing mean and variance across location years. The most prominent QTL was Qkernel.CORE.4D on chromosome 4D at approximately 212 cM, which influenced the mean levels of all traits. QTL were identified that influenced trait variance but not mean, trait mean only and both.

Download Full-text

Genome-wide association and prediction studies using a grapevine diversity panel give insights into the genetic architecture of several traits of interest

10.1101/2020.09.10.290890 ◽

2020 ◽

Author(s):

T Flutre ◽

L Le Cunff ◽

A Fodor ◽

A Launay ◽

C Romieu ◽

...

Keyword(s):

Yield Components ◽

Prediction Accuracy ◽

Genetic Architecture ◽

Genetic Variance ◽

Breeding Programs ◽

Stress Indicator ◽

Genome Wide ◽

Aroma Precursors ◽

Variance Explained ◽

Response Variables

SummaryTo cope with the challenges facing agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennials, but requires to understand the genetic architecture of important traits. To go beyond QTL mapping in bi-parental crosses, we exploited a diverse panel of 279 Vitis vinifera L. cultivars. This panel planted in five blocks in the vineyard was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. Such an experimental design allowed us to reliably assess the genotypic values for most traits. The panel was genotyped for 60k SNPs by combining an 18K microarray and sequencing (GBS). Marker densification via GBS markedly increased the proportion of genetic variance explained by SNPs, and two multi-SNP models identified QTLs not found by a SNP-by-SNP model. This led to 489 reliable QTLs using the combined microarray-GBS SNPs for 41% more response variables than a SNP-by-SNP model applied to microarray-only SNPs, and many QTLs were new compared to the results from bi-parental crosses. Prediction accuracy ranging from 0.14 to 0.84 for 80% of the response variables was promising for genomic selection, and provided insights into the genetic architecture of each trait when put in perspective with the number of QTLs and heritability.

Download Full-text

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

BMC Genomics ◽

10.1186/s12864-020-07288-1 ◽

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.

Download Full-text

Genetic variability and genome-wide association analysis of flavor and texture in cooked beans (Phaseolus vulgaris L.)

Theoretical and Applied Genetics ◽

10.1007/s00122-020-03745-3 ◽

2021 ◽

Author(s):

Amber Bassett ◽

Kelvin Kamfwa ◽

Daniel Ambachew ◽

Karen Cichy

Keyword(s):

Genetic Variability ◽

Seed Coat ◽

Principal Component ◽

Breeding Programs ◽

Flavor Intensity ◽

Genome Wide ◽

White Bean ◽

The Usa ◽

New Varieties ◽

End Use

Abstract Key message Cooked bean flavor and texture vary within and across 20 Andean seed types; SNPs are significantly associated with total flavor, beany, earthy, starchy, bitter, seed-coat perception, and cotyledon texture. Abstract Common dry beans are a nutritious food recognized as a staple globally, but their consumption is low in the USA. Improving bean flavor and texture through breeding has the potential to improve consumer acceptance and suitability for new end-use products. Little is known about genetic variability and inheritance of bean sensory characteristics. A total of 430 genotypes of the Andean Diversity Panel representing twenty seed types were grown in three locations, and cooked seeds were evaluated by a trained sensory panel for flavor and texture attribute intensities, including total flavor, beany, vegetative, earthy, starchy, sweet, bitter, seed-coat perception, and cotyledon texture. Extensive variation in sensory attributes was found across and within seed types. A set of genotypes was identified that exhibit extreme attribute intensities generally stable across all three environments. seed-coat perception and total flavor intensity had the highest broad-sense heritability (0.39 and 0.38, respectively), while earthy and vegetative intensities exhibited the lowest (0.14 and 0.15, respectively). Starchy and sweet flavors were positively correlated and highest in white bean genotypes according to principal component analysis. SNPs associated with total flavor intensity (six SNPs across three chromosomes), beany (five SNPs across four chromosomes), earthy (three SNPs across two chromosomes), starchy (one SNP), bitter (one SNP), seed-coat perception (three SNPs across two chromosomes), and cotyledon texture (two SNPs across two chromosomes) were detected. These findings lay a foundation for incorporating flavor and texture in breeding programs for the development of new varieties that entice growers, consumers, and product developers alike.

Download Full-text

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

Theoretical and Applied Genetics ◽

10.1007/s00122-021-03906-y ◽

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.

Download Full-text

Breeding of High Cooking and Eating Quality in Rice by Marker-Assisted Backcrossing (MABc) Using KASP Markers

Plants ◽

10.3390/plants10040804 ◽

2021 ◽

Vol 10 (4) ◽

pp. 804

Author(s):

Me-Sun Kim ◽

Ju-Young Yang ◽

Ju-Kyung Yu ◽

Yi Lee ◽

Yong-Jin Park ◽

...

Keyword(s):

Genetic Background ◽

Amylose Content ◽

Yield Potential ◽

Eating Quality ◽

Breeding Cycle ◽

Recurrent Parent ◽

Rice Varieties ◽

Breeding Programs ◽

Genome Wide ◽

Cooking And Eating Quality

The primary goals of rice breeding programs are grain quality and yield potential improvement. With the high demand for rice varieties of premium cooking and eating quality, we developed low-amylose content breeding lines crossed with Samgwang and Milkyqueen through the marker-assisted backcross (MABc) breeding program. Trait markers of the SSIIIa gene referring to low-amylose content were identified through an SNP mapping activity, and the markers were applied to select favorable lines for a foreground selection. To rapidly recover the genetic background of Samgwang (recurrent parent genome, RPG), 386 genome-wide markers were used to select BC1F1 and BC2F1 individuals. Seven BC2F1 lines with targeted traits were selected, and the genetic background recovery range varied within 97.4–99.1% of RPG. The amylose content of the selected BC2F2 grains ranged from 12.4–16.8%. We demonstrated the MABc using a trait and genome-wide markers, allowing us to efficiently select lines of a target trait and reduce the breeding cycle effectively. In addition, the BC2F2 lines confirmed by molecular markers in this study can be utilized as parental lines for subsequent breeding programs of high-quality rice for cooking and eating.

Download Full-text

Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus

Plants ◽

10.3390/plants10050890 ◽

2021 ◽

Vol 10 (5) ◽

pp. 890

Author(s):

Zifeng Ouyang ◽

Yimeng Wang ◽

Tiantian Ma ◽

Gisele Kanzana ◽

Fan Wu ◽

...

Keyword(s):

Group Method ◽

Ltr Retrotransposon ◽

Ltr Retrotransposons ◽

Important Data ◽

Breeding Programs ◽

Upgma Dendrogram ◽

Pair Group ◽

Medicinal Value ◽

Genome Wide ◽

Melilotus Albus

Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus.

Download Full-text

Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

Evolutionary Bioinformatics ◽

10.1177/1176934319889948 ◽

2019 ◽

Vol 15 ◽

pp. 117693431988994

Author(s):

Shulin Zhang ◽

Yaling Cai ◽

Jinggong Guo ◽

Kun Li ◽

Renhai Peng ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Genetic Relationships ◽

Phylogenetic Analyses ◽

Genotyping By Sequencing ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Breeding Programs ◽

Association Analyses ◽

Genome Wide ◽

Candidate Gene Locus

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

Download Full-text

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

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2016.0569 ◽

2016 ◽

Vol 283 (1835) ◽

pp. 20160569 ◽

Cited By ~ 52

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.

Download Full-text