A new genetic linkage map of barley (Hordeum vulgare L.) facilitates genetic dissection of height and spike length and angle

Islamovic, Emir; Obert, D. E.; Oliver, Rebekah E.; Marshall, Juliet M.; Miclaus, Kelci; Hang, A.; Chao, Shiaoman; Lazo, Gerard R.; Harrison, Stephen A.; Ibrahim, Amir M. H.; Jellen, Eric N.; Maughan, Peter J.; Brown, Raymond S.; Jackson, Eric W.

doi:10.1016/j.fcr.2013.06.001

Cited by 19 publications

(11 citation statements)

References 36 publications

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“… 8 . The chromosome location of btwd1 is different from the hcm1 gene (2HL) 29 , sdw3 gene (2HS) 31 , uzu gene (3HL) 8 12 29 32 33 , sdw1/denso geng (3HL) 8 14 29 34 35 , br2 (4H) 8 36 37 , ari-e gene (5HL) 29 , br1 gene (7HS) 8 36 37 , and also different from the plant height QTL on chromosome 1H 2 29 38 39 40 , 2H 2 29 39 41 42 , 3H 2 28 39 42 43 44 , 4H 38 39 40 43 45 46 , 5H 38 39 45 , 6H 2 45 , and 7H 29 38 39 42 43 47 , which further demonstrated that the btwd1 is a novel gene.…”

Section: Discussionmentioning

confidence: 98%

“…Constructing a high-density linkage map is a vital prerequisite for genetic analysis and efficient molecular breeding. For the past ten years there has been a surge in marker density and convergence toward consensus maps for barley 2 4 5 6 20 21 22 23 24 25 26 27 28 29 ( Table 3 ). In the previous published barley genetic maps, limited number of markers were included using traditional marker technologies such as RFLP, RAPD, DArT, SSR and EST based markers 4 5 20 21 30 .…”

Section: Discussionmentioning

confidence: 99%

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SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley

Ren

Wang

Liu

et al. 2016

Sci Rep

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A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley.

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Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley

Ren

Wang

Liu

et al. 2016

Sci Rep

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“…The SSR marker Bmac90 was associated with days to heading on chromosome 1H [ 61 ]. QTLs for main MSL were reported to be located on all seven linkage groups [ 16 , 22 , 56 – 58 , 62 , 63 ].…”

Section: Discussionmentioning

confidence: 99%

QTL underlying some agronomic traits in barley detected by SNP markers

et al. 2016

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BackgroundIncreasing the yield of barley (Hordeum vulgare L.) is a main breeding goal in developing barley cultivars. A high density genetic linkage map containing 1894 SNP and 68 SSR markers covering 1375.8 cM was constructed and used for mapping quantitative traits. A late-generation double haploid population (DH) derived from the Huaai 11 × Huadamai 6 cross was used to identify QTLs and QTL × environment interactions for ten traits affecting grain yield including length of main spike (MSL), spikelet number on main spike (SMS), spikelet number per plant (SLP), grain number per plant (GP), grain weight per plant (GWP), grain number per spike (GS), thousand grain weight (TGW), grain weight per spike (GWS), spike density (SPD) and spike number per plant (SP).ResultsIn single environment analysis using composite interval mapping (CIM), a total of 221 QTLs underlying the ten traits were detected in five consecutive years (2009–2013). The QTLs detected in each year were 50, 48, 41, 41 and 41 for the year 2009 to 2013. The QTLs associated with these traits were generally clustered on chromosome 2H, 4H and 7H.In multi-environment analysis, a total of 111 significant QTLs including 18 for MSL, 16 for SMS, 15 for SPD, 5 for SP, 4 for SLP, 14 for TGW, 5 for GP, 11 for GS, 8 for GWP, and 15 for GWS were detected in the five years. Most QTLs showed significant QTL × environment interactions (QEI), nine QTLs (qIMSL3-1, qIMSL4-1, qIMSL4-2, qIMSL6-1, qISMS7-1, qISPD2-7, qISPD7-1, qITGW3-1 and qIGWS4-3) were detected with minimal QEI effects and stable in different years. Among 111 QTLs,71 (63.40 %) QTLs were detected in both single and multiple environments.ConclusionsThree main QTL cluster regions associated with the 10 agronomic traits on chromosome 2H, 4H and 7H were detected. The QTLs for SMS, SLP, GP and GWP were located in the region near Vrs1 on chromosome 2H. The QTLs underlying SMS, SPD and SLP were clustered on chromosome 4H. On the terminal of chromosome 7H, there was a QTL cluster associated with TGW, SPD, GWP and GWS. The information will be useful for marker-assisted selection (MAS) in barley breeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0409-y) contains supplementary material, which is available to authorized users.

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“…The genetic linkage map was constructed using JMP Genomics 8.0 (SAS Institute) as described by [45] and [46]. The initial number of linkage groups (LGs) was identified using interactive hierarchical clustering and K-means clustering (automated radius K-means) by reducing the number of markers in the recombination and LG function.…”

Section: Linkage Map Construction and Qtl Analysismentioning

confidence: 99%

Genome-Wide Linkage Mapping of Quantitative Trait Loci for Late-Season Physiological and Agronomic Traits in Spring Wheat under Irrigated Conditions

Liu

Wang

et al. 2018

Agronomy

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Many late-season physiological traits affect grain yield in wheat, either directly or indirectly. However, information on the genetic control of yield-related traits is still limited. In this study, we aimed to identify quantitative trait loci (QTL) for canopy temperature and chlorophyll content index during anthesis (CTa and CCIa, respectively), the mid grain-filling stage (CTg1 and CCIg1, respectively), and the late grain-filling stage (CTg2 and CCIg2, respectively) as well as for plant height (PH), thousand kernels weight (TKW), and grain yield (GY) using genome-wide linkage mapping. To this end, a double haploid population derived from a cross between two high yielding wheat cultivars, UI Platinum and SY Capstone, was phenotyped in four irrigated environments and genotyped using the wheat 90K iSelect platform and simple sequence repeats. The genotypic data were used to construct a high-density genetic map of 43 linkage groups (LGs) with a total length of 3594.0 cm and a marker density of 0.37 cm. A total of 116 QTL for all nine traits was detected on 33 LGs, spreading to all wheat chromosomes, except for Chr. 7D. Of these, six QTL (CTa.ui-4B.1, Q.CTg1.ui-5B-2.1, Q.CTg2.ui-6B.1, Q.PH.ui-6A-2.1, Q.TKW.ui-2D-1, and Q.GY.ui-6B) were consistently detected in more than three irrigated environments, called as stable QTL. Additionally, we identified 26 QTL clusters for more than two traits, of which the top four were located on Chromosomes 4A-1, 1B-1, 5B-2, and 2D-1. Overall, the stable QTL significantly related with grain yield, QTL clusters, and linked molecular markers identified in this study, may be useful in marker-assisted selection in early generation and early growth stage for grain yield improvement.

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A new genetic linkage map of barley (Hordeum vulgare L.) facilitates genetic dissection of height and spike length and angle

Cited by 19 publications

References 36 publications

SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley

SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley

QTL underlying some agronomic traits in barley detected by SNP markers

Genome-Wide Linkage Mapping of Quantitative Trait Loci for Late-Season Physiological and Agronomic Traits in Spring Wheat under Irrigated Conditions

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