scholarly journals Functional Analysis of the “Green Revolution” Gene Photoperiod-1 and Its Selection Trends During Bread Wheat Breeding

2021 ◽  
Vol 12 ◽  
Author(s):  
Yongzhen Wu ◽  
Jiahui Liu ◽  
Guimei Hu ◽  
Huixian Xue ◽  
Huiyuan Xu ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Plant Height ◽  
Association Analysis ◽  
Green Revolution ◽  
Heading Date ◽  
Wheat Breeding ◽  
Grain Weight ◽  
Genome Wide Association ◽  
Thousand Grain Weight ◽  
Genome Wide

Flowering is central to the transformation of plants from vegetative growth to reproductive growth. The circadian clock system enables plants to sense the changes in the external environment and to modify the growth and development process at an appropriate time. Photoperiod-1 (Ppd-1), which is controlled by the output signal of the circadian clock, has played an important role in the wheat “Green Revolution.” In the current study, we systematically studied the relationship between Ppd-1 haplotypes and both wheat yield- and quality-related traits, using genome-wide association analysis and transgenic strategies, and found that highly appropriate haplotypes had been selected in the wheat breeding programs. Genome-wide association analysis showed that Ppd-1 is associated with significant differences in yield-related traits in wheat, including spike length (SL), heading date (HD), plant height (PH), and thousand-grain weight (TGW). Ppd-1-Hapl-A1 showed increased SL by 4.72–5.93%, whereas Ppd-1-Hapl-B1 and Ppd-1-Hapl-D1 displayed earlier HD by 0.58–0.75 and 1.24–2.93%, respectively, decreased PH by 5.64–13.08 and 13.62–27.30%, respectively, and increased TGW by 4.89–10.94 and 11.12–21.45%, respectively. Furthermore, the constitutive expression of the Ppd-D1 gene in rice significantly delayed heading date and resulted in reduced plant height, thousand-grain weight, grain width (GW), and total protein content. With reference to 40years of data from Chinese wheat breeding, it was found that the appropriate haplotypes Ppd-1-Hapl-A1, Ppd-1-Hapl-B1, and Ppd-1-Hapl-D1 had all been subjected to directional selection, and that their distribution frequencies had increased from 26.09, 60.00, and 52.00% in landraces to 42.55, 93.62, and 96.23% in wheat cultivars developed in the 2010s. A Ppd-B1 methylation molecular marker was also developed to assist molecular wheat breeding. This research is of significance for fully exploring the function of the Ppd-1 gene and its genetic resource diversity, to effectively use the most appropriate haplotypes and to improve crop yield and sustainability.

scholarly journals Genome-Wide Association Study in Rice Revealed a Novel Gene in Determining Plant Height and Stem Development, by Encoding a WRKY Transcription Factor

2021 ◽  
Vol 22 (15) ◽  
pp. 8192
Author(s):  
Xiaoshuang Wei ◽  
Hailian Zhou ◽  
Deying Xie ◽  
Jianguo Li ◽  
Mingchong Yang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Association Study ◽  
Plant Height ◽  
Stress Responses ◽  
Genome Wide Association Study ◽  
Heading Date ◽  
Wrky Transcription Factor ◽  
Genome Wide Association ◽  
Dwarf Phenotype ◽  
Genome Wide

Semi-dwarfism is a main agronomic trait in crop breeding. In this study, we performed genome-wide association study (GWAS) and identified a new quantitative trait nucleotide (QTN) for rice shoot length. The peak QTN (C/T) was located in the first coding region of a group III WRKY transcription factor OsWRKY21 (LOC_Os01g60640). Interestingly, further haplotype analysis showed that C/T difference only existed in the indica group but not in the japonica group, resulting in significant differences in plant height among the different indica rice varieties. OsWRKY21 was expressed in embryo, radicle, shoots, leaves, and stems. Most notably, overexpressing OsWRKY21 resulted in the semi-dwarf phenotype, early heading date and short internodes compared to the wild type, while the knockout mutant plants by CRISPR/Cas9 technology yielded the opposite. The overexpressing lines exhibited the decreased length of the cells near sclerenchyma epidermis, accompanied with the lower levels of indole-3-acetic acid (IAA) and gibberellin 3 (GA3), but increased levels of the abscisic acid (ABA) and salicylic acid (SA) in the internodes at heading stage. Moreover, the semi-dwarf phenotype could be fully rescued by exogenous GA3 application at seedling stage. The RNA-seq and qRT-PCR analysis confirmed the differential expression levels of genes in development and the stress responses in rice, including GA metabolism (GA20ox2, GA2ox6, and YABY1) and cell wall biosynthesis (CesA4, 7, and 9) and regulation (MYB103L). These data suggest the essential role of OsWRKY21 in regulation of internode elongation and plant height in rice.

scholarly journals A Genome-Wide Association Study Pinpoints Quantitative Trait Genes for Plant Height, Heading Date, Grain Quality, and Yield in Rye (Secale cereale L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Dörthe Siekmann ◽  
Gisela Jansen ◽  
Anne Zaar ◽  
Andrzej Kilian ◽  
Franz Joachim Fromme ◽  
...  
Keyword(s):  
Plant Height ◽  
Grain Quality ◽  
Genome Wide Association Study ◽  
Reference Genome ◽  
Protein Gene ◽  
Heading Date ◽  
Genome Wide Association ◽  
Hybrid Breeding ◽  
Quality Traits ◽  
Genome Wide

Rye is the only cross-pollinating Triticeae crop species. Knowledge of rye genes controlling complex-inherited traits is scarce, which, currently, largely disables the genomics assisted introgression of untapped genetic variation from self-incompatible germplasm collections in elite inbred lines for hybrid breeding. We report on the first genome-wide association study (GWAS) in rye based on the phenotypic evaluation of 526 experimental hybrids for plant height, heading date, grain quality, and yield in 2 years and up to 19 environments. We established a cross-validated NIRS calibration model as a fast, effective, and robust analytical method to determine grain quality parameters. We observed phenotypic plasticity in plant height and tiller number as a resource use strategy of rye under drought and identified increased grain arabinoxylan content as a striking phenotype in osmotically stressed rye. We used DArTseq™ as a genotyping-by-sequencing technology to reduce the complexity of the rye genome. We established a novel high-density genetic linkage map that describes the position of almost 19k markers and that allowed us to estimate a low genome-wide LD based on the assessed genetic diversity in elite germplasm. We analyzed the relationship between plant height, heading date, agronomic, as well as grain quality traits, and genotype based on 20k novel single-nucleotide polymorphism markers. In addition, we integrated the DArTseq™ markers in the recently established ‘Lo7' reference genome assembly. We identified cross-validated SNPs in ‘Lo7' protein-coding genes associated with all traits studied. These include associations of the WUSCHEL-related homeobox transcription factor DWT1 and grain yield, the DELLA protein gene SLR1 and heading date, the Ethylene overproducer 1-like protein gene ETOL1 and thousand-grain weight, protein and starch content, as well as the Lectin receptor kinase SIT2 and plant height. A Leucine-rich repeat receptor protein kinase and a Xyloglucan alpha-1,6-xylosyltransferase count among the cross-validated genes associated with water-extractable arabinoxylan content. This study demonstrates the power of GWAS, hybrid breeding, and the reference genome sequence in rye genetics research to dissect and identify the function of genes shaping genetic diversity in agronomic and grain quality traits of rye. The described links between genetic causes and phenotypic variation will accelerate genomics-enabled rye improvement.

Genome-wide Association Analysis of Plant Height in Rapeseed (Brassica napus)

2015 ◽  
Vol 41 (7) ◽  
pp. 1121 ◽  
Author(s):  
Min-Qiang TANG ◽  
Xiao-Hui CHENG ◽  
Chao-Bo TONG ◽  
Yue-Ying LIU ◽  
Chuan-Ji ZHAO ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Plant Height ◽  
Association Analysis ◽  
Genome Wide Association ◽  
Genome Wide Association Analysis ◽  
Genome Wide

scholarly journals Multi-Locus GWAS for Grain Weight-Related Traits Under Rain-Fed Conditions in Common Wheat (Triticum aestivum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Vijay Gahlaut ◽  
Vandana Jaiswal ◽  
Harindra S. Balyan ◽  
Arun Kumar Joshi ◽  
Pushpendra K. Gupta
Keyword(s):  
Genome Wide Association Study ◽  
Current Knowledge ◽  
Geometric Mean ◽  
Resistance Index ◽  
Wheat Breeding ◽  
Grain Weight ◽  
Genome Wide Association ◽  
Productivity Index ◽  
Tolerance Index ◽  
Genome Wide

In wheat, a multi-locus genome-wide association study (ML-GWAS) was conducted for the four grain weight-related traits (days to anthesis, grain filling duration, grain number per ear, and grain weight per ear) using data recorded under irrigated (IR) and rain-fed (RF) conditions. Seven stress-related indices were estimated for these four traits: (i) drought resistance index (DI), (ii) geometric mean productivity (GMP), (iii) mean productivity index (MPI), (iv) relative drought index (RDI), (v) stress tolerance index (STI), (vi) yield index, and (vii) yield stability index (YSI). The association panel consisted of a core collection of 320 spring wheat accessions representing 28 countries. The panel was genotyped using 9,627 single nucleotide polymorphisms (SNPs). The genome-wide association (GWA) analysis provided 30 significant marker-trait associations (MTAs), distributed as follows: (i) IR (15 MTAs), (ii) RF (14 MTAs), and (iii) IR+RF (1 MTA). In addition, 153 MTAs were available for the seven stress-related indices. Five MTAs co-localized with previously reported QTLs/MTAs. Candidate genes (CGs) associated with different MTAs were also worked out. Gene ontology (GO) analysis and expression analysis together allowed the selection of the two CGs, which may be involved in response to drought stress. These two CGs included: TraesCS1A02G331000 encoding RNA helicase and TraesCS4B02G051200 encoding microtubule-associated protein 65. The results supplemented the current knowledge on genetics for drought tolerance in wheat. The results may also be used for future wheat breeding programs to develop drought-tolerant wheat cultivars.

scholarly journals Genome-wide association analysis for lodging tolerance and plant height in a diverse European hexaploid oat collection

Euphytica ◽  
2017 ◽  
Vol 213 (8) ◽  
Author(s):  
Giorgio Tumino ◽  
Roeland E. Voorrips ◽  
Caterina Morcia ◽  
Roberta Ghizzoni ◽  
Christoph U. Germeier ◽  
...  
Keyword(s):  
Plant Height ◽  
Association Analysis ◽  
Genome Wide Association ◽  
Genome Wide Association Analysis ◽  
Genome Wide
Sign in / Sign up

Export Citation Format

Share Document