scholarly journals Genome-Wide Association Study on Seminal and Nodal Roots of Wheat Under Different Growth Environments

2021 ◽  
Vol 11 ◽  
Author(s):  
Fengdan Xu ◽  
Shulin Chen ◽  
Xiwen Yang ◽  
Sumei Zhou ◽  
Xu Chen ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Root Traits ◽  
Hydroponic Culture ◽  
Genome Wide Association ◽  
Seminal Root ◽  
Nodal Roots ◽  
Genome Wide ◽  
Nodal Root

The root of wheat consists of seminal and nodal roots. Comparatively speaking, fewer studies have been carried out on the nodal root system because of its disappearance at the early seedling stage under indoor environments. In this study, 196 accessions from the Huanghuai Wheat Region (HWR) were used to identify the characteristics of seminal and nodal root traits under different growth environments, including indoor hydroponic culture (IHC), outdoor hydroponic culture (OHC), and outdoor pot culture (OPC), for three growing seasons. The results indicated that the variation range of root traits in pot environment was larger than that in hydroponic environment, and canonical coefficients were the greatest between OHC and OPC (0.86) than those in other two groups, namely, IHC vs. OPC (0.48) and IHC vs. OHC (0.46). Most root traits were negatively correlated with spikes per area (SPA), grains per spike (GPS), and grain yield (GY), while all the seminal root traits were positively correlated with thousand-kernel weight (TKW). Genome-wide association study (GWAS) was carried out on root traits by using a wheat 660K SNP array. A total of 35 quantitative trait loci (QTLs)/chromosomal segments associated with root traits were identified under OPC and OHC. In detail, 11 and 24 QTLs were significantly associated with seminal root and nodal root traits, respectively. Moreover, 13 QTLs for number of nodal roots per plant (NRP) containing 14 stable SNPs, were distributed on chromosomes 1B, 2B, 3A, 4B, 5D, 6D, 7A, 7B, and Un. Based on LD and bioinformatics analysis, these QTLs may contain 17 genes closely related to NRP. Among them, TraesCS2B02G552500 and TraesCS7A02G428300 were highly expressed in root tissues. Moreover, the frequencies of favorable alleles of these 14 SNPs were confirmed to be less than 70% in the natural population, suggesting that the utilization of these superior genes in wheat root is still improving.

scholarly journals Genome-Wide Association Study on Root Traits Under Different Growing Environments in Wheat (Triticum aestivum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Fengdan Xu ◽  
Shulin Chen ◽  
Xiwen Yang ◽  
Sumei Zhou ◽  
Junsen Wang ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Root Traits ◽  
Hydroponic Culture ◽  
Genome Wide Association ◽  
Growth Stages ◽  
Genome Wide ◽  
A Genome ◽  
Pot Culture

Plant roots are critical for water and nutrient acquisition, environmental adaptation, and yield formation. Herein, 196 wheat accessions from the Huang-Huai Wheat Region of China were collected to investigate six root traits at seedling stage under three growing environments [indoor hydroponic culture (IHC), outdoor hydroponic culture (OHC), and outdoor pot culture (OPC)] and the root dry weight (RDW) under OPC at four growth stages and four yield traits in four environments. Additionally, a genome-wide association study was performed with a Wheat 660K SNP Array. The results showed that the root traits varied most under OPC, followed by those under both OHC and IHC, and root elongation under hydroponic culture was faster than that under pot culture. Root traits under OHC might help predict those under OPC. Moreover, root traits were significantly negatively correlated with grain yield (GY) and grains per spike (GPS), positively correlated with thousand-kernel weight (TKW), and weakly correlated with number of spikes per area (SPA). Twelve stable chromosomal regions associated with the root traits were detected on chromosomes 1D, 2A, 4A, 4B, 5B, 6D, and unmapped markers. Among them, a stable chromosomal interval from 737.85 to 742.00 Mb on chromosome 4A, which regulated total root length (TRL), was identified under three growing environments. Linkage disequilibrium (LD) blocks were used to identify 27 genes related to root development. Three genes TraesCS4A02G484200, TraesCS4A02G484800, TraesCS4A02G493800, and TraesCS4A02G493900, are involved in cell elongation and differentiation and expressed at high levels in root tissues. Another vital co-localization interval on chromosome 5B (397.72–410.88 Mb) was associated with not only RDW under OHC and OPC but also TKW.

scholarly journals Genome-wide association study on root traits under different cultivation patterns in wheat

2020 ◽  
Author(s):  
Fengdan Xu ◽  
Shulin Chen ◽  
Xiwen Yang ◽  
Sumei Zhou ◽  
Xu Chen ◽  
...  
Keyword(s):  
Association Study ◽  
Root Development ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Root Traits ◽  
Hydroponic Culture ◽  
Genome Wide Association ◽  
Growth Stages ◽  
Genome Wide

Abstract Background Roots are critical for water and nutrient acquisition, environmental adaptation and yield formation. Results Here, 196 accessions from Yellow and Huai Winter Wheat Region (YHW) of China were collected for investigating the performance of six root traits under three cultivation patterns—Indoor Hydroponic Culture (IHC), Outdoor Hydroponic Culture (OHC) and Outdoor Pot Culture (OPC) at different growth stages—for three consecutive years. In the same growth period, OPC root traits always varied greatly, followed by OHC and IHC. The correlation coefficients between IHC and OPC at stooling stage (SS) were lower (0.016 ~ 0.278) than those between OHC and OPC (0.29 ~ 0.378). Root traits were negatively correlated grain yield (GY), the canonical correlation coefficient between root traits and yield was the highest (0.232) at SS. Genome-wide association study (GWAS) was furtherly conducted by a wheat 660K SNP array. It was revealed that 1105 SNP loci were significantly associated with root traits. A co-localized chromosomal segment regulating total root length (TRL) was detected on chromosome 4A, spanning from 737.85 to 742.00 Mb, under different cultivation patterns at stooling stage. Another co-localization region regulating total root area (TRA) was detected on chromosome 5A, an approximately 6.17 ~ 18.76 Mb region at SS, wintering stage (WT) and jointing stage (JS) under OPC. LD analysis and blast comparison revealed 27 and 31 genes related to root development were found from these two segments, respectively. Among them, TraesCS4A02G493900, TraesCS4A02G494200, TraesCS5A02G021700, TraesCS5A02G021800 and TraesCS5A02G011600 were predicted to be highly expressed in root. Conclusion This work could deepen our understanding of the molecular mechanisms of root development under different cultivation patterns in common wheat.

scholarly journals Genome-wide association study identifies loci and candidate genes for internal organ weights in Simmental beef cattle

2018 ◽  
Vol 50 (7) ◽  
pp. 523-531 ◽  
Author(s):  
Bingxing An ◽  
Jiangwei Xia ◽  
Tianpeng Chang ◽  
Xiaoqiao Wang ◽  
Jian Miao ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Genome Wide Association ◽  
Heart Weight ◽  
Spleen Weight ◽  
Internal Organs ◽  
Genome Wide ◽  
A Genome

Cattle internal organs as accessible raw materials have a long history of being widely used in beef processing, feed and pharmaceutical industry. These traits not only are of economic interest to breeders, but they are intrinsically linked to many valuable traits, such as growth, health, and productivity. Using the Illumina Bovine HD 770K SNP array, we performed a genome-wide association study for heart weight, liver weight, spleen weight, lung weight, and kidney weight in 1,217 Simmental cattle. In our research, 38 significant single nucleotide polymorphisms (SNPs) ( P < 1.49 × 10−6) were identified for five internal organ weight traits. These SNPs are within or near 13 genes, and some of them have been reported previously, including NDUFAF4, LCORL, BT.94996, SLIT2, FAM184B, LAP3, BBS12, MECOM, CD300LF, HSD17B3, TLR4, MXI1, and MB21D2. In addition, we detected four haplotype blocks on BTA6 containing 18 significant SNPs associated with spleen weight. Our results offer worthy insights into understanding the genetic mechanisms of internal organs' development, with potential application in breeding programs of Simmental beef cattle.

scholarly journals Transcriptomic and Genome-wide Association Study Reveal Long Noncoding RNAs Responding to Nitrogen Deficiency in Maize

2020 ◽  
Author(s):  
PENG MA ◽  
Xiao Zhang ◽  
Bowen Luo ◽  
Zhen Chen ◽  
Xuan He ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Nitrogen Deficiency ◽  
Snp Array ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Genome Wide Association ◽  
Rna Seq ◽  
Genome Wide ◽  
A Genome

Abstract Background: Long noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited.Results: Here, we surveyed the lncRNAs and miRNAs in maize inbred line P178 leaves and roots at the seedling stage under high-nitrogen and low-nitrogen conditions using lncRNA-Seq and small RNA-Seq. A total of 894 differentially expressed lncRNAs and 38 different miRNAs were identified. Co-expression analysis found two lncRNAs and four lncRNA-targets could competitively combine with ZmmiR159 and ZmmiR164, respectively. To dissect the genetic regulatory by which lncRNAs might enable adaptation to limited nitrogen availability. An association mapping panel containing a high-density single–nucleotide polymorphism (SNP) array (56,110 SNPs) combined with variable LN resistance-related phenotypes obtained from hydroponics was used for a genome-wide association study (GWAS). By combining GWAS and RNA-Seq, 170 differently expressed lncRNAs within the range of significant markers were screened. Moreover, 40 consistently LN-responsive genes including those involved in glutamine biosynthesis and nitrogen acquisition in root were identified. Transient expression assays in Nicotiana benthamiana demonstrated LNC_002923 could inhabit ZmmiR159-guided cleavage of Zm00001d015521. Conclusions: These lncRNAs containing trait-associated significant SNPs could consider to be related to root development and nutrient utilization. Taken together, the results of our study can provide new insights into the potential regulatory roles of lncRNAs in response to LN stress, and give valuable information for further screening of candidates as well as the improvement of maize regarding LN-responsive resistance.

scholarly journals Genome-Wide Association Study of Brown Rot (Monilinia spp.) Tolerance in Peach

2021 ◽  
Vol 12 ◽  
Author(s):  
Wanfang Fu ◽  
Cassia da Silva Linge ◽  
Ksenija Gasic
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genetic Resistance ◽  
Snp Array ◽  
Brown Rot ◽  
Severity Index ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Fruit Decay ◽  
Genomic Regions

Brown rot, caused by Monilinia spp., is one of the most important diseases on stone fruit worldwide. Severe yield loss can be caused by pre- and post-harvest fruit decay. Although some degree of tolerance has been reported in peach and almond, the genetic resistance in peach cultivars is still lacking. To date, only few genomic regions associated with brown rot response in fruit skin and flesh have been detected in peach. Previous studies suggested brown rot tolerance in peach being a polygenic quantitative trait. More information is needed to uncover the genetics behind brown rot tolerance in peach. To identify the genomic regions in peach associated with this trait, 26 cultivars and progeny from 9 crosses with ‘Bolinha’ sources of tolerance, were phenotyped across two seasons (2015 and 2016) for brown rot disease severity index in wounded and non-wounded fruits and genotyped using a newly developed 9+9K peach SNP array. Genome wide association study using single- and multi-locus methods by GAPIT version 3, mrMLM 4.0, GAPIT and G Model, revealed 14 reliable SNPs significantly associated with brown rot infection responses in peach skin (10) and flesh (4) across whole genome except for chromosome 3. Candidate gene analysis within the haplotype regions of the detected markers identified 25 predicted genes associated with pathogen infection response/resistance. Results presented here facilitate further understanding of genetics behind brown rot tolerance in peach and provide an important foundation for DNA-assisted breeding.

Genome-Wide association study identifies new elements on the genetic basis of quality-related traits in wheat across multiple environments

2020 ◽  
Author(s):  
Zhien Pu ◽  
Xueling Ye ◽  
Yang Li ◽  
Zehou Liu ◽  
Bingxin Shi ◽  
...  
Keyword(s):  
Association Study ◽  
Complex Traits ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Mixed Linear Model ◽  
Genome Wide Association ◽  
Phenotypic Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Abstract Backgrounds: Grain protein concentration (GPC), grain starch concentration (GSC), and wet gluten concentration (WGC) are complex traits that determine nutrient concentration, end-use quality, and yield in wheat. To identify the elite and stable loci or genomic regions conferring high GPC, GSC, and WGC, a genome-wide association study (GWAS) based on a mixed linear model (MLM) was performed using 55K single nucleotide polymorphism (SNP) array in a panel of 236 wheat accessions, including 160 commercial varieties and 76 landraces, derived from Sichuan Province, China. The panel was evaluated for GPC, GSC, and WGC at four different fields. Results: Phenotypic analysis showed variation in GPC, GSC, and WGC among the different genotypes and environments. GWAS identified 12 quantitative trait loci (QTL) (-log10(P) > 2.5) associated with these three quality traits in at least two environments and located on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 5D, and 7D; the phenotypic variation explained (PVE) by these QTL ranged from 4.2% to 10.7%. Among these, three, seven, and two QTL are associated with GPC, GSC, and WGC, respectively; five QTL (QGsc.sicau-1BL, QGsc.sicau-1DS, QGsc.sicau-2DL.1, QGsc.sicau-2DL.2, QWgc.sicau-5DL) were defined potentially novel Compared with the previously reported QTLs/genes by linkage or association mapping, 5 QTLs (QGsc.sicau-1BL, QGsc.sicau-1DS, QGsc.sicau-2DL.1, QGsc.sicau-2DL.2, QWgc.sicau-5DL) were potentially novel. Furthermore, 21 presumptive candidate genes, which are involved in the metabolism or transportation of all kinds of carbohydrates, photosynthesis, programmed cell death, the balance of abscisic acid and ethylene, within these potentially novel genomic regions were predicted. Conclusions: This study provided new genetic resources and valuable genetic information of nutritional quality to broaden the genetic background and laid the molecular foundation for marker-assisted selection in wheat quality breeding.

scholarly journals Transcriptomic and genome-wide association study reveal long noncoding RNAs responding to nitrogen deficiency in maize

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Peng Ma ◽  
Xiao Zhang ◽  
Bowen Luo ◽  
Zhen Chen ◽  
Xuan He ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Nitrogen Deficiency ◽  
Snp Array ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Genome Wide Association ◽  
Rna Seq ◽  
Genome Wide ◽  
A Genome

Abstract Background Long noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited. Results Here, we surveyed the lncRNAs and miRNAs in maize inbred line P178 leaves and roots at the seedling stage under high-nitrogen (HN) and low-nitrogen (LN) conditions using lncRNA-Seq and small RNA-Seq. A total of 894 differentially expressed lncRNAs and 38 different miRNAs were identified. Co-expression analysis found that two lncRNAs and four lncRNA-targets could competitively combine with ZmmiR159 and ZmmiR164, respectively. To dissect the genetic regulatory by which lncRNAs might enable adaptation to limited nitrogen availability, an association mapping panel containing a high-density single–nucleotide polymorphism (SNP) array (56,110 SNPs) combined with variable LN tolerant-related phenotypes obtained from hydroponics was used for a genome-wide association study (GWAS). By combining GWAS and RNA-Seq, 170 differently expressed lncRNAs within the range of significant markers were screened. Moreover, 40 consistently LN-responsive genes including those involved in glutamine biosynthesis and nitrogen acquisition in root were identified. Transient expression assays in Nicotiana benthamiana demonstrated that LNC_002923 could inhabit ZmmiR159-guided cleavage of Zm00001d015521. Conclusions These lncRNAs containing trait-associated significant SNPs could consider to be related to root development and nutrient utilization. Taken together, the results of our study can provide new insights into the potential regulatory roles of lncRNAs in response to LN stress, and give valuable information for further screening of candidates as well as the improvement of maize resistance to LN stress.

scholarly journals Genome-wide association screening and verification of potential genes associated with root architectural traits in maize (Zea mays L.) at multiple seedling stages

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Abdourazak Alio Moussa ◽  
Ajmal Mandozai ◽  
Yukun Jin ◽  
Jing Qu ◽  
Qi Zhang ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Root Traits ◽  
Significant Snps ◽  
Root Systems ◽  
Genome Wide Association ◽  
Growth Stages ◽  
Genome Wide ◽  
Maize Varieties ◽  
Architectural Traits

Abstract Background Breeding for new maize varieties with propitious root systems has tremendous potential in improving water and nutrients use efficiency and plant adaptation under suboptimal conditions. To date, most of the previously detected root-related trait genes in maize were new without functional verification. In this study, seven seedling root architectural traits were examined at three developmental stages in a recombinant inbred line population (RIL) of 179 RILs and a genome-wide association study (GWAS) panel of 80 elite inbred maize lines through quantitative trait loci (QTL) mapping and genome-wide association study. Results Using inclusive composite interval mapping, 8 QTLs accounting for 6.44–8.83 % of the phenotypic variation in root traits, were detected on chromosomes 1 (qRDWv3-1-1 and qRDW/SDWv3-1-1), 2 (qRBNv1-2-1), 4 (qSUAv1-4-1, qSUAv2-4-1, and qROVv2-4-1), and 10 (qTRLv1-10-1, qRBNv1-10-1). GWAS analysis involved three models (EMMAX, FarmCPU, and MLM) for a set of 1,490,007 high-quality single nucleotide polymorphisms (SNPs) obtained via whole genome next-generation sequencing (NGS). Overall, 53 significant SNPs with a phenotypic contribution rate ranging from 5.10 to 30.2 % and spread all over the ten maize chromosomes exhibited associations with the seven root traits. 17 SNPs were repeatedly detected from at least two growth stages, with several SNPs associated with multiple traits stably identified at all evaluated stages. Within the average linkage disequilibrium (LD) distance of 5.2 kb for the significant SNPs, 46 candidate genes harboring substantial SNPs were identified. Five potential genes viz. Zm00001d038676, Zm00001d015379, Zm00001d018496, Zm00001d050783, and Zm00001d017751 were verified for expression levels using maize accessions with extreme root branching differences from the GWAS panel and the RIL population. The results showed significantly (P < 0.001) different expression levels between the outer materials in both panels and at all considered growth stages. Conclusions This study provides a key reference for uncovering the complex genetic mechanism of root development and genetic enhancement of maize root system architecture, thus supporting the breeding of high-yielding maize varieties with propitious root systems.

scholarly journals Genome-Wide Association Study Reveals Candidate Genes Involved in Fruit Trait Variation in Persian Walnut (Juglans regia L.)

2021 ◽  
Vol 11 ◽  
Author(s):  
Anthony Bernard ◽  
Julie Crabier ◽  
Armel S. L. Donkpegan ◽  
Annarita Marrano ◽  
Fabrice Lheureux ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Fruit Quality ◽  
Genome Wide Association Study ◽  
Juglans Regia ◽  
Snp Array ◽  
Germplasm Collection ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

Elucidating the genetic determinants of fruit quality traits in walnut is essential to breed new cultivars meeting the producers and consumers’ needs. We conducted a genome-wide association study (GWAS) using multi-locus models in a panel of 170 accessions of Juglans regia from the INRAE walnut germplasm collection, previously genotyped using the AxiomTMJ. regia 700K SNP array. We phenotyped the panel for 25 fruit traits related to morphometrics, shape, volume, weight, ease of cracking, and nutritional composition. We found more than 60 marker-trait associations (MTAs), including a highly significant SNP associated with nut face diameter, nut volume and kernel volume on chromosome 14, and 5 additional associations were detected for walnut weight. We proposed several candidate genes involved in nut characteristics, such as a gene coding for a beta-galactosidase linked to several size-related traits and known to be involved in fruit development in other species. We also confirmed associations on chromosomes 5 and 11 with nut suture strength, recently reported by the University of California, Davis. Our results enhance knowledge of the genetic control of important agronomic traits related to fruit quality in walnut, and pave the way for the development of molecular markers for future assisted selection.

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