Genome-wide association study using cellular traits identifies a new regulator of root development in Arabidopsis

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.

Download Full-text

Genome-Wide Association Study of Root System Development at Seedling Stage in Rice

Genes ◽

10.3390/genes11121395 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1395

Author(s):

Hongjia Zhang ◽

Mar Lar San ◽

Seong-Gyu Jang ◽

Ja-Hong Lee ◽

Na-Eun Kim ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Root Development ◽

Genome Wide Association Study ◽

Germplasm Collection ◽

Genome Wide Association ◽

Matrix Analysis ◽

Root Weight ◽

Breeding Programs ◽

Genome Wide

Root network structure plays a crucial role in growth and development processes in rice. Longer, more branched root structures help plants to assimilate water and nutrition from soil, support robust plant growth, and improve resilience to stresses such as disease. Understanding the molecular basis of root development through screening of root-related traits in rice germplasms is critical to future rice breeding programs. This study used a small germplasm collection of 137 rice varieties chosen from the Korean rice core set (KRICE_CORE) to identify loci linked to root development. Two million high-quality single nucleotide polymorphisms (SNPs) were used as the genotype, with maximum root length (MRL) and total root weight (TRW) in seedlings used as the phenotype. Genome-wide association study (GWAS) combined with Principal Components Analysis (PCA) and Kinship matrix analysis identified four quantitative trait loci (QTLs) on chromosomes 3, 6, and 8. Two QTLs were linked to MRL and two were related to TRW. Analysis of Linkage Disequilibrium (LD) decay identified a 230 kb exploratory range for detection of candidate root-related genes. Candidates were filtered using RNA-seq data, gene annotations, and quantitative real-time PCR (qRT-PCR), and five previously characterized genes related to root development were identified, as well as four novel candidate genes. Promoter analysis of candidate genes showed that LOC_Os03g08880 and LOC_Os06g13060 contained SNPs with the potential to impact gene expression in root-related promoter motifs. Haplotype analysis of candidate genes revealed diverse haplotypes that were significantly associated with phenotypic variation. Taken together, these results indicate that LOC_Os03g08880 and LOC_Os06g13060 are strong candidate genes for root development functions. The significant haplotypes identified in this study will be beneficial in future breeding programs for root improvement.

Download Full-text