scholarly journals Construction of Consensus Genetic Map With Applications in Gene Mapping of Wheat (Triticum aestivum L.) Using 90K SNP Array

2021 ◽  
Vol 12 ◽  
Author(s):  
Pingping Qu ◽  
Jiankang Wang ◽  
Weie Wen ◽  
Fengmei Gao ◽  
Jindong Liu ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Genetic Information ◽  
Physical Map ◽  
Recombinant Inbred Lines ◽  
Snp Array ◽  
Triticum Aestivum L ◽  
Kernel Weight ◽  
Consensus Map ◽  
Phenotypic Data ◽  
Putative Gene

Wheat is one of the most important cereal crops worldwide. A consensus map combines genetic information from multiple populations, providing an effective alternative to improve the genome coverage and marker density. In this study, we constructed a consensus map from three populations of recombinant inbred lines (RILs) of wheat using a 90K single nucleotide polymorphism (SNP) array. Phenotypic data on plant height (PH), spike length (SL), and thousand-kernel weight (TKW) was collected in six, four, and four environments in the three populations, and then used for quantitative trait locus (QTL) mapping. The mapping results obtained using the constructed consensus map were compared with previous results obtained using individual maps and previous studies on other populations. A simulation experiment was also conducted to assess the performance of QTL mapping with the consensus map. The constructed consensus map from the three populations spanned 4558.55 cM in length, with 25,667 SNPs, having high collinearity with physical map and individual maps. Based on the consensus map, 21, 27, and 19 stable QTLs were identified for PH, SL, and TKW, much more than those detected with individual maps. Four PH QTLs and six SL QTLs were likely to be novel. A putative gene called TraesCS4D02G076400 encoding gibberellin-regulated protein was identified to be the candidate gene for one major PH QTL located on 4DS, which may enrich genetic resources in wheat semi-dwarfing breeding. The simulation results indicated that the length of the confidence interval and standard errors of the QTLs detected using the consensus map were much smaller than those detected using individual maps. The consensus map constructed in this study provides the underlying genetic information for systematic mapping, comparison, and clustering of QTL, and gene discovery in wheat genetic study. The QTLs detected in this study had stable effects across environments and can be used to improve the wide adaptation of wheat cultivars through marker-assisted breeding.

scholarly journals QTL Mapping and Validation for Kernel Area and Circumference in Common Wheat via High-Density SNP-Based Genotyping

2021 ◽  
Vol 12 ◽  
Author(s):  
Tianheng Ren ◽  
Tao Fan ◽  
Shulin Chen ◽  
Xia Ou ◽  
Yongyan Chen ◽  
...  
Keyword(s):  
Recombinant Inbred Lines ◽  
Snp Array ◽  
Interval Mapping ◽  
Mapping Method ◽  
Kernel Weight ◽  
Kernel Size ◽  
Specific Pcr ◽  
Wheat Kernel ◽  
Ril Population ◽  
Stable Qtls

As an important component, 1,000 kernel weight (TKW) plays a significant role in the formation of yield traits of wheat. Kernel size is significantly positively correlated to TKW. Although numerous loci for kernel size in wheat have been reported, our knowledge on loci for kernel area (KA) and kernel circumference (KC) remains limited. In the present study, a recombinant inbred lines (RIL) population containing 371 lines genotyped using the Wheat55K SNP array was used to map quantitative trait loci (QTLs) controlling the KA and KC in multiple environments. A total of 54 and 44 QTLs were mapped by using the biparental population or multienvironment trial module of the inclusive composite interval mapping method, respectively. Twenty-two QTLs were considered major QTLs. BLAST analysis showed that major and stable QTLs QKc.sau-6A.1 (23.12–31.64 cM on 6A) for KC and QKa.sau-6A.2 (66.00–66.57 cM on 6A) for KA were likely novel QTLs, which explained 22.25 and 20.34% of the phenotypic variation on average in the 3 year experiments, respectively. Two Kompetitive allele-specific PCR (KASP) markers, KASP-AX-109894590 and KASP-AX-109380327, were developed and tightly linked to QKc.sau-6A.1 and QKa.sau-6A.2, respectively, and the genetic effects of the different genotypes in the RIL population were successfully confirmed. Furthermore, in the interval where QKa.sau-6A.2 was located on Chinese Spring and T. Turgidum ssp. dicoccoides reference genomes, only 11 genes were found. In addition, digenic epistatic QTLs also showed a significant influence on KC and KA. Altogether, the results revealed the genetic basis of KA and KC and will be useful for the marker-assisted selection of lines with different kernel sizes, laying the foundation for the fine mapping and cloning of the gene(s) underlying the stable QTLs detected in this study.

scholarly journals Dissection of Genetic Basis Underpinning Kernel Weight-Related Traits in Common Wheat

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 713
Author(s):  
Shunda Li ◽  
Liang Wang ◽  
Yaning Meng ◽  
Yuanfeng Hao ◽  
Hongxin Xu ◽  
...  
Keyword(s):  
Recombinant Inbred Lines ◽  
Wheat Yield ◽  
Snp Array ◽  
Kernel Weight ◽  
Yield Potential ◽  
Phenotypic Variance ◽  
Genetic Dissection ◽  
Single Nucleotide ◽  
Grain Width ◽  
Potential Improvement

Genetic dissection kernel weight-related traits is of great significance for improving wheat yield potential. As one of the three major yield components of wheat, thousand kernel weight (TKW) was mainly affected by grain length (GL) and grain width (GW). To uncover the key loci for these traits, we carried out a quantitative trait loci (QTL) analysis of an F6 recombinant inbred lines (RILs) population derived from a cross of Henong 5290 (small grain) and 06Dn23 (big grain) with a 50 K single nucleotide polymorphism (SNP) array. A total of 17 stable and big effect QTL, including 5 for TKW, 8 for GL and 4 for GW, were detected on the chromosomes 1B, 2A, 2B, 2D, 4B, 5A, 6A and 6D, respectively. Among these, there were two co-located loci for three traits that were mapped on the chromosome 4BS and 6AL. The QTL on 6AL was the most stable locus and explained 15.4–24.8%, 4.1–8.8% and 15.7–24.4% of TKW, GW and GL variance, respectively. In addition, two more major QTL of GL were located on chromosome arm 2BL and 2DL, accounting for 9.7–17.8% and 13.6–19.8% of phenotypic variance, respectively. In this study, we found one novel co-located QTL associated with GL and TKW in 2DL, QGl.haaf-2DL.2/QTkw.haaf-2DL.2, which could explain 13.6–19.8% and 9.8–10.7% phenotypic variance, respectively. Genetic regions and linked markers of these stable QTL will help to further refine mapping of the corresponding loci and marker-assisted selection (MAS) breeding for wheat grain yield potential improvement.

QTL mapping of 1000-kernel weight, kernel length, and kernel width in bread wheat (Triticum aestivum L.)

2010 ◽  
Vol 51 (4) ◽  
pp. 421-429 ◽  
Author(s):  
P. Ramya ◽  
A. Chaubal ◽  
K. Kulkarni ◽  
L. Gupta ◽  
N. Kadoo ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Qtl Mapping ◽  
Bread Wheat ◽  
Triticum Aestivum L ◽  
Kernel Weight ◽  
Kernel Width ◽  
Kernel Length

scholarly journals Identification of Novel Genomic Regions for Biofortification Traits Using an SNP Marker-Enriched Linkage Map in Wheat (Triticum aestivum L.)

2021 ◽  
Vol 8 ◽  
Author(s):  
Gopalareddy Krishnappa ◽  
Nagenahalli Dharmegowda Rathan ◽  
Deepmala Sehgal ◽  
Arvind Kumar Ahlawat ◽  
Santosh Kumar Singh ◽  
...  
Keyword(s):  
Recombinant Inbred Lines ◽  
Aegilops Tauschii ◽  
Iron Concentration ◽  
Wheat Variety ◽  
Triticum Aestivum L ◽  
Grain Protein Content ◽  
Kernel Weight ◽  
Snp Markers ◽  
Wheat Varieties ◽  
Genomic Regions

Micronutrient and protein malnutrition is recognized among the major global health issues. Genetic biofortification is a cost-effective and sustainable strategy to tackle malnutrition. Genomic regions governing grain iron concentration (GFeC), grain zinc concentration (GZnC), grain protein content (GPC), and thousand kernel weight (TKW) were investigated in a set of 163 recombinant inbred lines (RILs) derived from a cross between cultivated wheat variety WH542 and a synthetic derivative (Triticum dicoccon PI94624/Aegilops tauschii [409]//BCN). The RIL population was genotyped using 100 simple-sequence repeat (SSR) and 736 single nucleotide polymorphism (SNP) markers and phenotyped in six environments. The constructed genetic map had a total genetic length of 7,057 cM. A total of 21 novel quantitative trait loci (QTL) were identified in 13 chromosomes representing all three genomes of wheat. The trait-wise highest number of QTL was identified for GPC (10 QTL), followed by GZnC (six QTL), GFeC (three QTL), and TKW (two QTL). Four novel stable QTL (QGFe.iari-7D.1, QGFe.iari-7D.2, QGPC.iari-7D.2, and QTkw.iari-7D) were identified in two or more environments. Two novel pleiotropic genomic regions falling between Xgwm350–AX-94958668 and Xwmc550–Xgwm350 in chromosome 7D harboring co-localized QTL governing two or more traits were also identified. The identified novel QTL, particularly stable and co-localized QTL, will be validated to estimate their effects on different genetic backgrounds for subsequent use in marker-assisted selection (MAS). Best QTL combinations were identified by the estimation of additive effects of the stable QTL for GFeC, GZnC, and GPC. A total of 11 RILs (eight for GZnC and three for GPC) having favorable QTL combinations identified in this study can be used as potential donors to develop bread wheat varieties with enhanced micronutrients and protein.

scholarly journals QTL mapping for total grain anthocyanin content and 1000-kernel weight in barley recombinant inbred lines population

2019 ◽  
Vol 46 (1) ◽  
pp. 52-61
Author(s):  
Tao YANG ◽  
Xiao-Meng YANG ◽  
Juan DU ◽  
Kazim Ali Muhammad ◽  
Xia LI ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Kernel Weight ◽  
Anthocyanin Content

scholarly journals Consensus Genetic Linkage Map Construction Based on One Common Parental Line for QTL Mapping in Wheat

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 227
Author(s):  
Xin Hu ◽  
Yingquan Zhang ◽  
Jingjuan Zhang ◽  
Shahidul Islam ◽  
Maoyun She ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Positional Cloning ◽  
Coat Color ◽  
Physical Map ◽  
Wheat Breeding ◽  
Snp Markers ◽  
Genetic Maps ◽  
Parental Line ◽  
Seed Color ◽  
Consensus Map

The consensus map is used for the verification of marker order, quantitative trait locus (QTL) mapping and molecular marker-assisted selection (MAS) in wheat breeding. In this study, a wheat consensus genetic map named as Sp7A_G7A, was constructed using 5643 SNP markers in two double haploid (DH) populations of Spitfire × Bethlehem-7AS (Sp7A) and Gregory × Bethlehem-7AS (G7A), covering 4376.70 cM of 21 chromosomes (chr) with an average interval of 0.78 cM. The collinearity of the linkage maps with the consensus map of Con_map_Wang2014 and the physical map of wheat reference genome (IWGSC RefSeq v1.0) were analyzed based on the Spearman rank correlation coefficients. As results, the three constructed genetic maps of Sp7A, G7A and Sp7A_G7A showed high collinearity with the Con_map_Wang2014 and the physical map, and importantly, the collinearity level between our constructed maps and the wheat physical map is higher than that between the Con_map_Wang2014 and the physical map. The seed coat color QTL detected in both populations under multiple environments were on the region (745.73–760.14 Mbp) of the seed color gene R-B1/Tamyb10-B1 (TraesCS3B02G515900, 3B: 757,918,264–757,920,082 bp). The validated consensus map will be beneficial for QTL mapping, positional cloning, meta-QTL analysis and wheat breading.

scholarly journals Identification of QTLs for resistance to leaf and stem rusts in bread wheat (Triticum aestivum L.) using a mapping population of ‘Pamyati Azieva × Paragon’

2019 ◽  
Vol 23 (7) ◽  
pp. 887-895 ◽  
Author(s):  
Y. Genievskaya ◽  
Y. Fedorenko ◽  
A. Sarbayev ◽  
A. Amalova ◽  
S. Abugalieva ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Bread Wheat ◽  
Mapping Population ◽  
Recombinant Inbred Lines ◽  
Snp Array ◽  
Initial Step ◽  
Triticum Aestivum L ◽  
Field Trials ◽  
Snp Markers ◽  
The North

Leaf rust (LR) and stem rust (SR) are harmful fungal diseases of bread wheat (Triticum aestivum L.). The purpose of this study was to identify QTLs for resistance to LR and SR that are effective in two wheat-growing regions of Kazakhstan. To accomplish this task, a population of recombinant inbred lines (RILs) of ‘Pamyati Azieva × Paragon’ was grown in the northern and southeastern parts of Kazakhstan, phenotyped for LR/SR severities, and analyzed for key yield components. The study revealed a negative correlation between disease severity and plant productivity in both areas. The mapping population was genotyped using a 20,000 Illumina SNP array. A total of 4595 polymorphic SNP markers were further selected for linkage analysis after filtering based on missing data percentage and segregation distortion. Windows QTL Cartographer was applied to identify QTLs associated with LR and SR resistances in the RIL mapping population studied. Two QTLs for LR resistance and eight for SR resistance were found in the north, and the genetic positions of eight of them have matched the positions of the known Lr and Sr genes, while two QTLs for SR were novel. In the southeast, eight QTLs for LR and one for SR were identified in total. The study is an initial step of the genetic mapping of LR and SR resistance loci of bread wheat in Kazakhstan. Field trials in two areas of the country and the genotyping of the selected mapping population have allowed identification of key QTLs that will be effective in regional breeding projects for better bread wheat productivity.

scholarly journals QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 604
Author(s):  
Paolo Vitale ◽  
Fabio Fania ◽  
Salvatore Esposito ◽  
Ivano Pecorella ◽  
Nicola Pecchioni ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Recombinant Inbred Lines ◽  
Snp Array ◽  
Heading Date ◽  
Tiller Number ◽  
Genetic Maps ◽  
Yield Potential ◽  
Adaptation To Climate Change ◽  
Map Resolution ◽  
Mapping Populations

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F2 and F2-derived F3 families) and late (F6 and F7, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F2 and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F2 mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.

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