Large scale genome-wide association study reveals that drought induced lodging in grain sorghum is associated with plant height and traits linked to carbon remobilisation

AbstractSorghum is generally grown in water limited conditions and often lodges under post-anthesis drought, which reduces yield and quality. Due to its complexity, our understanding on the genetic control of lodging is very limited. We dissected the genetic architecture of lodging in grain sorghum through genome-wide association study (GWAS) on 2308 unique hybrids grown in 17 Australian sorghum trials over 3 years. The GWAS detected 213 QTL, the majority of which showed a significant association with leaf senescence and plant height (72% and 71% respectively). Only 16 lodging QTL were not associated with either leaf senescence or plant height. The high incidence of multi-trait association for the lodging QTL indicates that lodging in grain sorghum is mainly associated with plant height and traits linked to carbohydrate remobilisation. This result supported the selection for stay-green (delayed leaf senescence) to reduce lodging susceptibility, rather than selection for short stature and lodging resistance per se, which likely reduces yield. Additionally, our data suggested a protective effect of stay-green on weakening the association between lodging susceptibility and plant height. Our study also showed that lodging resistance might be improved by selection for stem composition but was unlikely to be improved by selection for classical resistance to stalk rots.Key messageWe detected 213 lodging QTL and demonstrated that drought induced stem lodging in grain sorghum is substantially associated with stay-green and plant height, suggesting a critical role of carbon remobilisation.

Download Full-text

Large-scale genome-wide association study reveals that drought-induced lodging in grain sorghum is associated with plant height and traits linked to carbon remobilisation

Theoretical and Applied Genetics ◽

10.1007/s00122-020-03665-2 ◽

2020 ◽

Vol 133 (11) ◽

pp. 3201-3215

Author(s):

Xuemin Wang ◽

Emma Mace ◽

Yongfu Tao ◽

Alan Cruickshank ◽

Colleen Hunt ◽

...

Keyword(s):

Association Study ◽

Plant Height ◽

Large Scale ◽

Genome Wide Association Study ◽

Grain Sorghum ◽

Genome Wide Association ◽

Genome Wide

Download Full-text

Candidate genes screening for plant height and the first branch height based on QTL mapping and genome-wide association study in rapessed (<italic>Brassica napus</italic> L.)

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2020.94067 ◽

2019 ◽

Vol 46 (2) ◽

pp. 214-227

Author(s):

Cun-Min QU ◽

Jia-Na LI ◽

Zhi-You CHEN ◽

Kun LU ◽

Qiang HUO ◽

...

Keyword(s):

Brassica Napus ◽

Qtl Mapping ◽

Association Study ◽

Candidate Genes ◽

Plant Height ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide

Download Full-text

Genome-Wide Association Study Identified Novel Candidate Loci/Genes Affecting Lodging Resistance in Rice

Genes ◽

10.3390/genes12050718 ◽

2021 ◽

Vol 12 (5) ◽

pp. 718

Author(s):

Bingxin Meng ◽

Tao Wang ◽

Yi Luo ◽

Deze Xu ◽

Lanzhi Li ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Association Analysis ◽

Genome Wide Association Study ◽

Flag Leaf ◽

Genome Wide Association ◽

Lodging Resistance ◽

Leaf Type ◽

Stem Strength ◽

Genome Wide

Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag leaf angle/FLA, Flag leaf width/FLW, leaf-rolling/LFR and SPAD/Soil, and plant analyzer development) using a diverse panel of 550 accessions and evaluated over two years. Genome-wide association study (GWAS) using 4,076,837 high-quality single-nucleotide polymorphisms (SNPs) identified 89 QTLs for the nine traits. Next, through “gene-based association analysis, haplotype analysis, and functional annotation”, the scope was narrowed down step by step. Finally, we identified 21 candidate genes in 9 important QTLs that included four reported genes (TUT1, OsCCC1, CFL1, and ACL-D), and seventeen novel candidate genes. Introgression of alleles, which are beneficial for both stem strength and leaf type, or pyramiding stem strength alleles and leaf type alleles, can be employed for LR breeding. All in all, the experimental data and the identified candidate genes in this study provide a useful reference for the genetic improvement of rice LR.

Download Full-text

Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

10.21203/rs.2.17481/v1 ◽

2019 ◽

Author(s):

Waltram Ravelombola ◽

Jun Qin ◽

Ainong Shi ◽

Fengmin Wang ◽

Yan Feng ◽

...

Keyword(s):

Association Study ◽

Genomic Selection ◽

Candidate Genes ◽

Plant Height ◽

Seed Weight ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Snp Markers ◽

Genome Wide Association ◽

Genome Wide

Abstract Background Soybean [ Glycine max (L.) Merr.] is a legume of great interest worldwide. Enhancing genetic gain for agronomic traits via molecular approaches has been long considered as the main task for soybean breeders and geneticists. The objectives of this study were to evaluate maturity, plant height, seed weight, and yield in a diverse soybean accession panel, to conduct a genome-wide association study (GWAS) for these traits and identify SNP markers associated with the four traits, and to assess genomic selection (GS) accuracy. Results A total of 250 soybean accessions were evaluated for maturity, plant height, seed weight, and yield over three years. This panel was genotyped with a total of 10,259 high quality SNPs postulated from genotyping by sequencing (GBS). GWAS was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model, and GS was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that a total of 20, 31, 37, 31, and 23 SNPs were significantly associated with the average 3-year data for maturity, plant height, seed weight, and yield, respectively; some significant SNPs were mapped into previously described loci ( E2 , E4 , and Dt1 ) affecting maturity and plant height in soybean and a new locus mapped on chromosome 20 was significantly associated with plant height; Glyma.10g228900 , Glyma.19g200800 , Glyma.09g196700 , and Glyma.09g038300 were candidate genes found in the vicinity of the top or the second best SNP for maturity, plant height, seed weight, and yield, respectively; a 11.5-Mb region of chromosome 10 was associated with both seed weight and yield; and GS accuracy was trait-, year-, and population structure-dependent. Conclusions The SNP markers identified from this study for plant height, maturity, seed weight and yield can be used to improve the four agronomic traits through marker-assisted selection (MAS) and GS in soybean breeding programs. After validation, the candidate genes can be transferred to new cultivars using SNP markers through MAS. The high GS accuracy has confirmed that the four agronomic traits can be selected in molecular breeding through GS.

Download Full-text