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.

scholarly journals Genetic dissection of grain architecture-related traits in a winter wheat population

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Matías Schierenbeck ◽  
Ahmad M. Alqudah ◽  
Ulrike Lohwasser ◽  
Rasha A. Tarawneh ◽  
María Rosa Simón ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Allelic Variation ◽  
Wheat Yield ◽  
Snp Array ◽  
Significant Snps ◽  
Kernel Weight ◽  
Yield Potential ◽  
Oxidoreductase Activity ◽  
Global Food Security ◽  
Kernel Length

Abstract Background The future productivity of wheat (T. aestivum L.) as the most grown crop worldwide is of utmost importance for global food security. Thousand kernel weight (TKW) in wheat is closely associated with grain architecture-related traits, e.g. kernel length (KL), kernel width (KW), kernel area (KA), kernel diameter ratio (KDR), and factor form density (FFD). Discovering the genetic architecture of natural variation in these traits, identifying QTL and candidate genes are the main aims of this study. Therefore, grain architecture-related traits in 261 worldwide winter accessions over three field-year experiments were evaluated. Results Genome-wide association analysis using 90K SNP array in FarmCPU model revealed several interesting genomic regions including 17 significant SNPs passing false discovery rate threshold and strongly associated with the studied traits. Four of associated SNPs were physically located inside candidate genes within LD interval e.g. BobWhite_c5872_589 (602,710,399 bp) found to be inside TraesCS6A01G383800 (602,699,767–602,711,726 bp). Further analysis reveals the four novel candidate genes potentially involved in more than one grain architecture-related traits with a pleiotropic effects e.g. TraesCS6A01G383800 gene on 6A encoding oxidoreductase activity was associated with TKW and KA. The allelic variation at the associated SNPs showed significant differences betweeen the accessions carying the wild and mutated alleles e.g. accessions carying C allele of BobWhite_c5872_589, TraesCS6A01G383800 had significantly higher TKW than the accessions carying T allele. Interestingly, these genes were highly expressed in the grain-tissues, demonstrating their pivotal role in controlling the grain architecture. Conclusions These results are valuable for identifying regions associated with kernel weight and dimensions and potentially help breeders in improving kernel weight and architecture-related traits in order to increase wheat yield potential and end-use quality.

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.

scholarly journals Identification of quantitative trait loci for kernel traits in a wheat cultivar Chuannong16

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jian Ma ◽  
Han Zhang ◽  
Shuiqin Li ◽  
Yaya Zou ◽  
Ting Li ◽  
...  
Keyword(s):  
Genetic Map ◽  
Quantitative Trait ◽  
Agronomic Traits ◽  
Snp Array ◽  
Kernel Weight ◽  
Phenotypic Variance ◽  
Kernel Length ◽  
Kasp Marker ◽  
Kernel Traits ◽  
Major Qtl

Abstract Background Kernel length (KL), kernel width (KW) and thousand-kernel weight (TKW) are key agronomic traits in wheat breeding. Chuannong16 (‘CN16’) is a commercial cultivar with significantly longer kernels than the line ‘20828’. To identify and characterize potential alleles from CN16 controlling KL, the previously developed recombinant inbred line (RIL) population derived from the cross ‘20828’ × ‘CN16’ and the genetic map constructed by the Wheat55K SNP array and SSR markers were used to perform quantitative trait locus/loci (QTL) analyses for kernel traits. Results A total of 11 putative QTL associated with kernel traits were identified and they were located on chromosomes 1A (2 QTL), 2B (2 QTL), 2D (3 QTL), 3D, 4A, 6A, and 7A, respectively. Among them, three major QTL, QKL.sicau-2D, QKW.sicau-2D and QTKW.sicau-2D, controlling KL, KW and TKW, respectively, were detected in three different environments. Respectively, they explained 10.88–18.85%, 17.21–21.49% and 10.01–23.20% of the phenotypic variance. Further, they were genetically mapped in the same interval on chromosome 2DS. A previously developed kompetitive allele-specific PCR (KASP) marker KASP-AX-94721936 was integrated in the genetic map and QTL re-mapping finally located the three major QTL in a 1- cM region flanked by AX-111096297 and KASP-AX-94721936. Another two co-located QTL intervals for KL and TKW were also identified. A few predicted genes involved in regulation of kernel growth and development were identified in the intervals of these identified QTL. Significant relationships between kernel traits and spikelet number per spike and anthesis date were detected and discussed. Conclusions Three major and stably expressed QTL associated with KL, KW, and TKW were identified. A KASP marker tightly linked to these three major QTL was integrated. These findings provide information for subsequent fine mapping and cloning the three co-localized major QTL for kernel traits.

scholarly journals Detection of Quantitative Trait Loci (QTL) Associated with the Fruit Morphology of Tomato

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1117
Author(s):  
Pragya Adhikari ◽  
James McNellie ◽  
Dilip R. Panthee
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Recombinant Inbred Lines ◽  
Tomato Fruit ◽  
Snp Array ◽  
Fruit Shape ◽  
Phenotypic Variance ◽  
Fruit Morphology ◽  
Trait Loci ◽  
Shape And Size

Tomato (Solanum lycopersicum L.) is the second most-consumed vegetable in the world. The market value and culinary purpose of tomato are often determined by fruit size and shape, which makes the genetic improvement of these traits a priority for tomato breeders. The main objective of the study was to detect quantitative trait loci (QTL) associated with the tomato fruit shape and size. The use of elite breeding materials in the genetic mapping studies will facilitate the detection of genetic loci of direct relevance to breeders. We performed QTL analysis in an intra-specific population of tomato developed from a cross between two elite breeding lines NC 30P × NC-22L-1(2008) consisting of 110 recombinant inbred lines (RIL). The precision software Tomato Analyzer (TA) was used to measure fruit morphology attributes associated with fruit shape and size traits. The RIL population was genotyped with the SolCAP 7720 SNP array. We identified novel QTL controlling elongated fruit shape on chromosome 10, explaining up to 24% of the phenotypic variance. This information will be useful in improving tomato fruit morphology traits.

scholarly journals Genetic dissection of yield-related traits and mid-parent heterosis for those traits in maize (Zea mays L.)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Qiang Yi ◽  
Yinghong Liu ◽  
Xianbin Hou ◽  
Xiangge Zhang ◽  
Hui Li ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Recombinant Inbred Lines ◽  
Kernel Weight ◽  
Genetic Dissection ◽  
Hybrid Mapping ◽  
Maize Breeding ◽  
Phenotypic Variations ◽  
Selection For ◽  
Genomic Regions ◽  
Mapping Populations

Abstract Background Utilization of heterosis in maize could be critical in maize breeding for boosting grain yield. However, the genetic architecture of heterosis is not fully understood. To dissect the genetic basis of yield-related traits and heterosis in maize, 301 recombinant inbred lines derived from 08 to 641 × YE478 and 298 hybrids from the immortalized F2 (IF2) population were used to map quantitative trait loci (QTLs) for nine yield-related traits and mid-parent heterosis. Results We observed 156 QTLs, 28 pairs of loci with epistatic interaction, and 10 significant QTL × environment interactions in the inbred and hybrid mapping populations. The high heterosis in F1 and IF2 populations for kernel weight per ear (KWPE), ear weight per ear (EWPE), and kernel number per row (KNPR) matched the high percentages of QTLs (over 50%) for those traits exhibiting overdominance, whereas a notable predominance of loci with dominance effects (more than 70%) was observed for traits that show low heterosis such as cob weight per ear (CWPE), rate of kernel production (RKP), ear length (EL), ear diameter (ED), cob diameter, and row number (RN). The environmentally stable QTL qRKP3–2 was identified across two mapping populations, while qKWPE9, affecting the trait mean and the mid-parent heterosis (MPH) level, explained over 18% of phenotypic variations. Nine QTLs, qEWPE9–1, qEWPE10–1, qCWPE6, qEL8, qED2–2, qRN10–1, qKWPE9, qKWPE10–1, and qRKP4–3, accounted for over 10% of phenotypic variation. In addition, QTL mapping identified 95 QTLs that were gathered together and integrated into 33 QTL clusters on 10 chromosomes. Conclusions The results revealed that (1) the inheritance of yield-related traits and MPH in the heterotic pattern improved Reid (PA) × Tem-tropic I (PB) is trait-dependent; (2) a large proportion of loci showed dominance effects, whereas overdominance also contributed to MPH for KNPR, EWPE, and KWPE; (3) marker-assisted selection for markers at genomic regions 1.09–1.11, 2.04, 3.08–3.09, and 10.04–10.05 contributed to hybrid performance per se and heterosis and were repeatedly reported in previous studies using different heterotic patterns is recommended.

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 Mapping QTL for spike fertility related traits in two double haploid wheat (Triticum aestivum L.) populations

2020 ◽  
Author(s):  
Nicole Pretini ◽  
Leonardo S. Vanzetti ◽  
Ignacio I. Terrile ◽  
Guillermo Donaire ◽  
Fernanda G. González
Keyword(s):  
Double Haploid ◽  
Snp Array ◽  
Triticum Aestivum L ◽  
Yield Potential ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Grain Number Per Spike ◽  
Fertility Traits ◽  
Major Qtl ◽  
Selection Of

AbstractIn breeding programs, the selection of cultivars with the highest yield potential consisted in the selection of the yield per se, which resulted in cultivars with a higher grain number per spike (GN) and occasionally higher grain weight (GW) (main numerical components of the yield). This task could be facilitated with the use of molecular markers such us single nucleotide polymorphism (SNP). In this study, quantitative trait loci (QTL) for GW, GN and spike fertility traits related to GN determination were mapped using two double haploid (DH) populations (Baguette Premium 11 x BioINTA 2002 and Baguette 19 x BioINTA 2002, BP11xB2002 and B19xB2002). Both populations were genotyped with the iSelect 90K SNP array and evaluated in four (BP11xB19) or five (B19xB2002) environments. We identify a total of 305 QTL for 14 traits, however 28 QTL for 12 traits were considered significant with an R2 > 10% and stable for being present at least in three environments. There were detected eight hotspot regions on chromosomes 1A, 2B, 3A, 5A, 5B, 7A and 7B were at least two major QTL sheared confident intervals. QTL on two of these regions have previously been described, but the other six regions were never observed, suggesting that these regions would be novel. The R5A1 (QSL.perg-5A, QCN.perg-5A,QGN.perg-5A) and R5A.2 (QFFTS.perg-5A, QGW.perg-5A) regions together with the QGW.perg-6B resulted in a final higher yield suggesting them to have high relevance as candidates to be used in MAS to improve yield.Author contribution statementKey message28 stable and major QTL for 12 traits associated to spike fertility, GN and GW were detected. Two regions on 5A Ch., and QGW.perg-6B showed direct pleiotropic effects on yield.

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 A High-Density Genetic Linkage Map of SLAFs and QTL Analysis of Grain Size and Weight in Barley (Hordeum vulgare L.)

2020 ◽  
Vol 11 ◽  
Author(s):  
Yunxia Fang ◽  
Xiaoqin Zhang ◽  
Xian Zhang ◽  
Tao Tong ◽  
Ziling Zhang ◽  
...  
Keyword(s):  
Grain Size ◽  
Genetic Map ◽  
Genetic Linkage Map ◽  
Recombinant Inbred Lines ◽  
High Density ◽  
Phenotypic Variance ◽  
Thousand Grain Weight ◽  
Hordeum Vulgare L ◽  
Specific Locus ◽  
Grain Width

Grain size is an important agronomic trait determines yield in barley, and a high-density genetic map is helpful to accurately detect quantitative trait loci (QTLs) related to grain traits. Using specific-locus amplified fragment sequencing (SLAF-seq) technology, a high-density genetic map was constructed with a population of 134 recombinant inbred lines (RILs) deriving from a cross between Golden Promise (GP) and H602, which contained 12,635 SLAFs with 26,693 SNPs, and spanned 896.74 cM with an average interval of 0.07 cM on seven chromosomes. Based on the map, a total of 16 QTLs for grain length (GL), grain width and thousand-grain weight were detected on 1H, 2H, 4H, 5H, and 6H. Among them, a major QTL locus qGL1, accounting for the max phenotypic variance of 16.7% was located on 1H, which is a new unreported QTL affecting GL. In addition, the other two QTLs, qGL5 and qTGW5, accounting for the max phenotypic variances of 20.7 and 21.1%, respectively, were identified in the same region, and sequencing results showed they are identical to HvDep1 gene. These results indicate that it is a feasible approach to construct a high-quality genetic map for QTL mapping by using SLAF markers, and the detected major QTLs qGL1, qGL5, and qTGW5 are useful for marker-assisted selection (MAS) of grain size in barley breeding.

scholarly journals Genetic Dissection of Seed Storability and Validation of Candidate Gene Associated with Antioxidant Capability in Rice (Oryza sativa L.)

2019 ◽  
Vol 20 (18) ◽  
pp. 4442 ◽  
Author(s):  
Yuan ◽  
Fan ◽  
Xia ◽  
Ding ◽  
Tian ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Oryza Sativa L ◽  
Recombinant Inbred Lines ◽  
Physiological Characteristic ◽  
Genetic Dissection ◽  
Isogenic Line ◽  
Single Nucleotide ◽  
F2 Population ◽  
Germination Ability ◽  
Seed Storability

Seed storability, defined as the ability to remain alive during storage, is an important agronomic and physiological characteristic, but the underlying genetic mechanism remains largely unclear. Here, we report quantitative trait loci (QTLs) analyses for seed storability using a high-density single nucleotide polymorphism linkage map in the backcross recombinant inbred lines that was derived from a cross of a japonica cultivar, Nipponbare, and an indica cultivar, 9311. Seven putative QTLs were identified for seed storability under natural storage, each explaining 3.6–9.0% of the phenotypic variation in this population. Among these QTLs, qSS1 with the 9311 alleles promoting seed storability was further validated in near-isogenic line and its derived-F2 population. The other locus (qSS3.1) for seed storability colocalized with a locus for germination ability under hydrogen peroxide, which is recognized as an oxidant molecule that causes lipid damage. Transgenic experiments validated that a candidate gene (OsFAH2) resides the qSS3.1 region controlling seed storability and antioxidant capability. Overexpression of OsFAH2 that encodes a fatty acid hydroxylase reduced lipid preoxidation and increased seed storability. These findings provide new insights into the genetic and physiological bases of seed storability and will be useful for the improvement of seed storability in rice.

Sign in / Sign up

Export Citation Format

Share Document