The stable loci on chromosomes 3A (AX_110657474), 5B (AX_109537496) and 7A (AX_89571435) identified in five or more environments and BLUE values by both methods are likely to be new. Find NCBI SARS-CoV-2 literature, sequence, and clinical content: https://www.ncbi.nlm.nih.gov/sars-cov-2/. 127, 2011–2028. The effects of dwarfing genes Rht1 and Rht2 on cellular dimensions and rate of leaf elongation in wheat. Because regulatory networks are highly interconnected, any expressed gene is likely to affect the regulation of core genes with a small effect size.

127, 2349–2358. PLoS One.

As GY related traits are mostly controlled by polygenes with small effect each, a genome-wide selection would be more powerful in gene discovery and pyramiding breeding with high-density genetic markers or genotyping by sequencing in future. Appl. Genome 48, 97–107. However, in the present study, co-localization of related loci and phenotypic correlations showed that TKW and KW were more highly correlated with GY than were SN and KNS. Development and evaluation of a barley 50k iSelect SNP array. (2020). The phenotypic traits GY, KNS, TKW, KL, KW, SL, HD, and PH were assessed in all six environments, whereas data for FLL and FLW and those for SN, SDW and UIL were obtained in five and four environments, respectively. Of the 35K SNP markers, 14,650 polymorphic mapped markers were used for LD analysis and subsequently for GWAS. 1989;64:683–90. G3 9, 2535–2547. Wurschum T, Langer SM, Longin CFH. Appl. Most significant association was seen for SR_34-1 at more than two loci (Table 3). Present study identified some GFD operating regions on 2B, 5B, 5D and 7D which validates previous [16, 17] findings and also underlined some additional regions on chromosomes 3B and 4A. J. Mol. Of 96 landraces in the panel, twenty-one were found resistant in field response against LR and eleven each against YR and SR. Landrace IC321998 (origin: Uttarakhand, India) was found resistant for all three rusts. The Impact of Agricultural Maintenance Research: The Case of Leaf Rust Resistance Breeding in CIMMYT-Related Spring Bread Wheat.

(B) YPP and RDG increased along with the combination of FMAs associated with YPP and RDG. The authors are grateful to Prof. R. A. McIntosh, Plant Breeding Institute, University of Sydney, for critical review of this manuscript. For each trait, the optimal number of PCs/covariates to include in GWAS models was determined through model selection using the Bayesian information criterion (BIC), with a maximum of four PCs tested. Heat stress induced ethylene production in developing wheat grains induces kernel abortion and increased maturation in a susceptible cultivar. HHS SNPs were called by setting minimum/maximum minor allele frequencies (MAF, 0.02 and 0.5) and minimum locus coverage was set at 0.2. A kinship matrix was also included in the GAPIT model to account for the relationships among individuals. In disease management practices, planting resistant varieties is the most economical, efficient, and ecologically acceptable tool to manage wheat rusts worldwide (McIntosh et al., 1995; Wiesner-Hanks and Nelson, 2016). Can. Front. Information from this scientific work will help wheat breeders for genetic improvement in the development of heat tolerant lines. https://doi.org/10.1371/journal.pone.0211730.g003. These results are more consistent with the comparison between methods in a simulation study [23]. With 29 SNPs for YR, the number of favorable alleles ranged from 6 to 26. Theor.

Since the SALs controlling PH and root depth are crucial for wheat improvement, we further analysed the breeding selection on common FMAs controlling YPP and PH simultaneously, and common FMAs for YPP and RDG. Primers to assay SNPs in the grain weight gene, TaGW2-6B, (S3 Table) were designed in house using the software Kraken (LGC Limited, London, UK), the available haplotype information [29] and the whole genome sequencing of 16 wheat varieties available through DAWN (Diversity Among Wheat geNomes, [30]). Sci. [66] pointed out that both GA-sensitive (Rht8) and GA-insensitive (Rht-B1 and Rht-D1) dwarfing alleles had effects on almost all investigated traits. Validation of marker rwgsnp7 in hexaploid wheat provided evidence that chromosome 6D harbors a homoeologous allele similar to that present on chromosome 6A for this marker (Sharma et al., 2019). 2005;110:865–80. Genet. For more information about PLOS Subject Areas, click Sukumaran S, Lopes M, Dreisigacker S, Reynolds M. Genome wide association mapping for grain weight in spring wheat across multiple environments. Two potential ASR loci QYr.ramp-1D.1 (AX-94508418: 1.03 Mb) and QYr.ramp-1D.3 (AX-94444583: 34.6 Mb) were observed both at distal and proximal regions of 1DS, respectively, in this study. BMC Plant Biology 6A (base pairs 15 202 326–16 883 226), 6B (base pairs 26 133 579–27 905 077) and 6D (base pairs 14 009 924–16 166 519), detected by both GLM and MLM, not only controlling YPP and CT, but exhibiting stable associations with root depth at different growth periods. These findings will be helpful in the development of a breeder friendly platform for the selection of high yielding wheat lines at high temperature areas. The phenotypic values in each environment and BLUE values were used for GWAS. doi: 10.1007/s00477-013-0821-z, Gangwar, O. P., Kumar, S., Bhardwaj, S. C., Kashyap, P. L., Prasad, P., and Khan, H. (2019).

Wu QH, Chen YX, Zhou SH, Fu L, Chen JJ, Xiao Y, Zhang D, Ouyang SH, Zhao XJ, Cui Y, Zhang DY, Liang Y, Wang ZZ, Xie JZ, Qin JX, Wang GX, Li DL, Huang YL, Yu MH, Lu P, Wang LL, Wang L, Wang H, Dang C, Li J, Zhang Y, Peng HR, Yuan CG, You MS, Sun QX, Wang JR, Wang LX, Luo MC, Han J, Liu ZY.

They are good parents to develop new high-yielding varieties. Google Scholar. We observed that the average frequency (FMAs/total marker alleles ratio for each peak SNP) of common FMAs associated with YPP and PH ranged from 50.4 to 68.9 %, higher than that of common FMAs associated with YPP and RDG (ranging from 26.0 to 35.8 %) (Fig. J. Mol. doi: 10.3835/plantgenome2015.03.0013, Wang, S., Wong, D., Forrest, K., Allen, A., Chao, S., Huang, B. E., et al. The selection of CMLM applied in this study was found suitable from the comparative study of different association models.

Wheat improvement in India: present status, emerging challenges and future prospects. [40], whereas 4B locus AX_110713957 is at a similar position to a QTL reported in Liu et al. Since not all landraces were found susceptible (Supplementary Table S3), they may still be beneficial in the identification of novel resistant alleles.

This could possibly remove the need to correct for population structure as one part of the phenotypic variation will only be associated with one cluster, due to the simultaneous nature of the testing approach. Rane J, Pannu RK, Sohu VS, Saini RS, Mishra B, Shoran J, et al. Serraj R, Krishnamurthy L, Kashiwagi J, Kumar J, Chandra S, Crouch JH. Plant Genome 9, 1–14. The K and Q (Kumar et al., 2020) matrices were considered as random and fixed components, respectively, to avoid any spurious associations caused by population structure. Bread wheat is an important crop cultivated on ~ 200 million hectares worldwide, and provides one fifth of the total needs of the global population [1,2,3]. Group I consisted of five accessions with deep-root FMAs of all peak SNPs in Co-6A, Co-6B and Co-6D; Group II consisted of five accessions with alternative shallow root marker alleles in these peak SNPs. As a function of genetic distance, the estimated r2− values for significant SNP marker pairs were plotted to understand the extent of LD.

Deployment of seedling (all-stage resistance), adult plant (non-race specific and race-specific) and slow rusting resistance is to create diversity for resistance (Bhardwaj et al., 2019b). Table 4. The genomic region 102.12–104.59 cM was observed to have ASR loci for each rust. Guo Z, Chen D, Alqudah AM, Roeder MS, Ganal MW, Schnurbusch T. Gyawali S, Harrington M, Durkin J, et al.

Breed. volume 19, Article number: 149 (2019)

https://doi.org/10.1371/journal.pone.0211730.g001. 2005;112:688–98. The Yellow and Huai River Valleys Wheat Zone (YHRVWZ) is the major wheat-producing region in China, and yield potential in this region has been improved over recent decades [4,5,6]. There were significant additive effects for each trait when favorable alleles were combined. [17], Cuthbert et al. 8:1792. doi: 10.3389/fpls.2017.01792. Dairy Sci. Genome-wide association analysis of agronomic traits in wheat under drought-stressed and non-stressed conditions. Plant Biotechnol. MS conducted the field condition phenotyping at Wellington, India. As proven by the LSD value for each trait, the effect of heat stress was significant, so the MTAs detected in both normal and heat-stressed conditions were underlined. The CMLM was observed as the best fit model. 2007;20:167–78. Analysis of phenotypic data for grain yield and related traits in the diverse panel. The accessions include 12 landraces, 36 advanced lines and 275 modern varieties, mainly planted in the Yellow and Huai River Valleys Facultative Wheat Zone and the Northern Winter Wheat Zone in China. [20] explained the variation in DH. Am. In NS condition, two markers on 2B explained 12 to 13% variation; Tiwari et al. Our objective was to use a high-density (GBS) platform through GWAS to identify chromosomal regions potentially associated with days to heading (DH), grain filling duration (GFD), plant height (PH), spikes per plant (SPP), grain number per spike (GNS), thousand kernel weight (TKW) and grain yield (GY) under normal and late sown conditions. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Deep-rooted accessions had lower CT and higher YPP than those with shallow roots, but no significant relationship was identified between root dry weight and shoot traits. The other four, which can be considered as QTL for yield per se (i.e. USA.gov. High-yielding varieties should have good adaptability to prevailing environments, strong resistance to abiotic and biotic stresses, and highly coordinated agronomic traits. [48], respectively. Funct. Shifting the limits in wheat research and breeding using a fully annotated reference genome. ), intermediate (mean + s.d. A decimal code for growth stages of cereals.