GWAS for Early-Establishment QTLs and Their Linkage to Major Phenology-Affecting Genes (, and ) in Bread Wheat

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2023 Jul 29

PMID 37510411

Authors

Md Farhad

Shashi B Tripathi

Ravi P Singh

Arun K Joshi

Pradeep K Bhati

Manish K Vishwakarma

Uttam Kumar

Affiliations

Soon will be listed here.

Abstract

Farmers in northern and central Indian regions prefer to plant wheat early in the season to take advantage of the remaining soil moisture. By planting crops before the start of the season, it is possible to extend the time frame for spring wheat. The early-wheat-establishment experiment began in the 2017 growing season at the Borlaug Institute for South Asia (BISA) in Ludhiana, India, and, after three years of intensive study, numerous agronomic, physiological, and yield data points were gathered. This study aimed to identify wheat lines suitable for early establishment through an analysis of the agro-morphological traits and the genetic mapping of associated genes or quantitative trait loci (QTLs). Advancing the planting schedule by two-three weeks proved to be advantageous in terms of providing a longer duration for crop growth and reducing the need for irrigation. This is attributed to the presence of residual soil moisture resulting from the monsoon season. Early sowing facilitated the selection of genotypes able to withstand early elevated temperatures and a prolonged phenological period. The ideotype, which includes increased photo-growing degree days for booting and heading, as well as a longer grain-filling period, is better suited to early planting than timely planting. Senescence was delayed in combination with a slower rate of canopy temperature rise, which was an excellent trait for early-adapted ideotypes. Thus, a novel approach to wheat breeding would include a screening of genotypes for early planting and an ideotype design with consistent and appropriate features. A genome-wide association study (GWAS) revealed multiple QTLs linked to early adaptation in terms of the yield and its contributing traits. Among them, 44 novel QTLs were also found along with known loci. Furthermore, the study discovered that the phenology regulatory genes, such as and , are in the same genomic region, thereby contributing to early adaptation.

Citing Articles

Reviewing the essential roles of remote phenotyping, GWAS and explainable AI in practical marker-assisted selection for drought-tolerant winter wheat breeding.

Chang-Brahim I, Koppensteiner L, Beltrame L, Bodner G, Saranti A, Salzinger J Front Plant Sci. 2024; 15:1319938.

PMID: 38699541 PMC: 11064034. DOI: 10.3389/fpls.2024.1319938.

References

Henderson C . Best linear unbiased estimation and prediction under a selection model. Biometrics. 1975; 31(2):423-47. View

Juliana P, Montesinos-Lopez O, Crossa J, Mondal S, Gonzalez Perez L, Poland J . Integrating genomic-enabled prediction and high-throughput phenotyping in breeding for climate-resilient bread wheat. Theor Appl Genet. 2018; 132(1):177-194. PMC: 6320358. DOI: 10.1007/s00122-018-3206-3. View

Zikhali M, Leverington-Waite M, Fish L, Simmonds J, Orford S, Wingen L . Validation of a 1DL earliness () flowering QTL in bread wheat (). Mol Breed. 2014; 34(3):1023-1033. PMC: 4162975. DOI: 10.1007/s11032-014-0094-3. View

Kumar U, Singh R, Dreisigacker S, Roder M, Crossa J, Huerta-Espino J . Juvenile Heat Tolerance in Wheat for Attaining Higher Grain Yield by Shifting to Early Sowing in October in South Asia. Genes (Basel). 2021; 12(11). PMC: 8622066. DOI: 10.3390/genes12111808. View

Diaz A, Zikhali M, Turner A, Isaac P, Laurie D . Copy number variation affecting the Photoperiod-B1 and Vernalization-A1 genes is associated with altered flowering time in wheat (Triticum aestivum). PLoS One. 2012; 7(3):e33234. PMC: 3310869. DOI: 10.1371/journal.pone.0033234. View

Metzker M . Sequencing technologies - the next generation. Nat Rev Genet. 2009; 11(1):31-46. DOI: 10.1038/nrg2626. View

Yan L, Helguera M, Kato K, Fukuyama S, Sherman J, Dubcovsky J . Allelic variation at the VRN-1 promoter region in polyploid wheat. Theor Appl Genet. 2004; 109(8):1677-86. DOI: 10.1007/s00122-004-1796-4. View

Peake A, Bell K, Fischer R, Gardner M, Das B, Poole N . Cultivar × Management Interaction to Reduce Lodging and Improve Grain Yield of Irrigated Spring Wheat: Optimising Plant Growth Regulator Use, N Application Timing, Row Spacing and Sowing Date. Front Plant Sci. 2020; 11:401. PMC: 7198859. DOI: 10.3389/fpls.2020.00401. View

Glaubitz J, Casstevens T, Lu F, Harriman J, Elshire R, Sun Q . TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One. 2014; 9(2):e90346. PMC: 3938676. DOI: 10.1371/journal.pone.0090346. View

10.

Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J . Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci U S A. 2003; 100(10):6263-8. PMC: 156360. DOI: 10.1073/pnas.0937399100. View

11.

Sehgal D, Autrique E, Singh R, Ellis M, Singh S, Dreisigacker S . Identification of genomic regions for grain yield and yield stability and their epistatic interactions. Sci Rep. 2017; 7:41578. PMC: 5286416. DOI: 10.1038/srep41578. View

12.

Gaut B, Long A . The lowdown on linkage disequilibrium. Plant Cell. 2003; 15(7):1502-6. PMC: 526043. DOI: 10.1105/tpc.150730. View

13.

Hanocq E, Laperche A, Jaminon O, Laine A, Le Gouis J . Most significant genome regions involved in the control of earliness traits in bread wheat, as revealed by QTL meta-analysis. Theor Appl Genet. 2006; 114(3):569-84. DOI: 10.1007/s00122-006-0459-z. View

14.

Kang H, Zaitlen N, Wade C, Kirby A, Heckerman D, Daly M . Efficient control of population structure in model organism association mapping. Genetics. 2008; 178(3):1709-23. PMC: 2278096. DOI: 10.1534/genetics.107.080101. View

15.

Yan L, Fu D, Li C, Blechl A, Tranquilli G, Bonafede M . The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proc Natl Acad Sci U S A. 2006; 103(51):19581-6. PMC: 1748268. DOI: 10.1073/pnas.0607142103. View

16.

Mohring J, Williams E, Piepho H . Inter-block information: to recover or not to recover it?. Theor Appl Genet. 2015; 128(8):1541-54. DOI: 10.1007/s00122-015-2530-0. View

17.

Maulana F, Ayalew H, Anderson J, Kumssa T, Huang W, Ma X . Genome-Wide Association Mapping of Seedling Heat Tolerance in Winter Wheat. Front Plant Sci. 2018; 9:1272. PMC: 6131858. DOI: 10.3389/fpls.2018.01272. View

18.

Elshire R, Glaubitz J, Sun Q, Poland J, Kawamoto K, Buckler E . A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011; 6(5):e19379. PMC: 3087801. DOI: 10.1371/journal.pone.0019379. View

19.

Bradbury P, Zhang Z, Kroon D, Casstevens T, Ramdoss Y, Buckler E . TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007; 23(19):2633-5. DOI: 10.1093/bioinformatics/btm308. View

20.

Poland J, Brown P, Sorrells M, Jannink J . Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One. 2012; 7(2):e32253. PMC: 3289635. DOI: 10.1371/journal.pone.0032253. View