Genetic identification and characterization of chromosomal regions for kernel length and width increase from tetraploid wheat

Abstract Background Improvement of wheat gercTriticum aestivum L.) yield could relieve global food shortages. Kernel size, as an important component of 1000-kernel weight (TKW), is always a significant consideration to improve yield for wheat breeders. Wheat related species possesses numerous elite genes that can be introduced into wheat breeding. It is thus vital to explore, identify, and introduce new genetic resources for kernel size from wheat wild relatives to increase wheat yield. Results In the present study, quantitative trait loci (QTL) for kernel length (KL) and width (KW) were detected in a recombinant inbred line (RIL) population derived from a cross between a wild emmer accession ‘LM001’ and a Sichuan endemic tetraploid wheat ‘Ailanmai’ using the Wheat 55 K single nucleotide polymorphism (SNP) array-based constructed linkage map and phenotype from six different environments. We identified eleven QTL for KL and KW including two major ones QKL.sicau-AM-3B and QKW.sicau-AM-4B, the positive alleles of which were from LM001 and Ailanmai, respectively. They explained 17.57 to 44.28% and 13.91 to 39.01% of the phenotypic variance, respectively. For these two major QTL, Kompetitive allele-specific PCR (KASP) markers were developed and used to successfully validate their effects in three F3 populations and two natural populations containing a panel of 272 Chinese wheat landraces and that of 300 Chinese wheat cultivars, respectively. QKL.sicau-AM-3B was located at 675.6–695.4 Mb on chromosome arm 3BL. QKW.sicau-AM-4B was located at 444.2–474.0 Mb on chromosome arm 4BL. Comparison with previous studies suggested that these two major QTL were likely new loci. Further analysis indicated that the positive alleles of QKL.sicau-AM-3B and QKW.sicau-AM-4B had a great additive effect increasing TKW by 6.01%. Correlation analysis between KL and other agronomic traits showed that KL was significantly correlated to spike length, length of uppermost internode, TKW, and flag leaf length. KW was also significantly correlated with TKW. Four genes, TRIDC3BG062390, TRIDC3BG062400, TRIDC4BG037810, and TRIDC4BG037830, associated with kernel development were predicted in physical intervals harboring these two major QTL on wild emmer and Chinese Spring reference genomes. Conclusions Two stable and major QTL for KL and KW across six environments were detected and verified in three biparental populations and two natural populations. Significant relationships between kernel size and yield-related traits were identified. KASP markers tightly linked the two major QTL could contribute greatly to subsequent fine mapping. These results suggested the application potential of wheat related species in wheat genetic improvement.

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Genetic identification and characterization of chromosomal regions for kernel length and width increase from tetraploid wheat

10.21203/rs.3.rs-397027/v1 ◽

2021 ◽

Author(s):

Jieguang Zhou ◽

Cong Li ◽

Jianing You ◽

Huaping Tang ◽

Yang Mu ◽

...

Keyword(s):

Related Species ◽

Tetraploid Wheat ◽

Natural Populations ◽

Wild Emmer ◽

Kernel Size ◽

Kernel Length ◽

Chromosome Arm ◽

Chinese Wheat ◽

Kasp Markers ◽

Major Qtl

Abstract Background: Improvement of wheat (Triticum aestivum L.) yield could relieve global food shortages. Kernel size, as an important component of 1000-kernel weight (TKW), is always a significant consideration to improve yield for wheat breeders. Wheat related species possesses numerous elite genes that can be introduced into wheat breeding. It is thus vital to explore, identify, and introduce new genetic resources for kernel size from wheat wild relatives to increase wheat yield.Results: In the present study, quantitative trait loci (QTL) for kernel length (KL) and width (KW) were detected in a recombinant inbred line (RIL) population derived from a cross between a wild emmer accession 'LM001' and a Sichuan endemic tetraploid wheat 'Ailanmai' using the Wheat 55K single nucleotide polymorphism (SNP) array-based constructed linkage map and phenotype from six different environments. We identified eleven QTL for KL and KW including two major ones QKL.sicau-AM-3B and QKW.sicau-AM-4B, the positive alleles of which were from LM001 and Ailanmai, respectively. They explained 17.57% to 44.28% and 13.91% to 39.01% of the phenotypic variance, respectively. For these two major QTL, Kompetitive allele-specific PCR (KASP) markers were developed and used to successfully validate their effects in three F3 populations and two natural populations containing a panel of 272 Chinese wheat landraces and that of 300 Chinese wheat cultivars, respectively. QKL.sicau-AM-3B was located at 666.2-685.9 Mb on chromosome arm 3BL. QKW.sicau-AM-4B was located at 639.7-696.4 Mb on chromosome arm 4BL. Comparison with previous studies suggested that these two major QTL were likely new loci. Further analysis indicated that the positive alleles of QKL.sicau-AM-3B and QKW.sicau-AM-4B had a great additive effect increasing TKW by 6.40%. Correlation analysis between KL and other agronomic traits showed that KL was significantly correlated to spike length, length of uppermost internode, TKW, and flag leaf length. KW was also significantly correlated with TKW. Four genes, TRIDC3BG062390, TRIDC3BG062400, TRIDC4BG037810, and TRIDC4BG037830, associated with kernel development were predicted in physical intervals harboring these two major QTL on wild emmer and Chinese Spring reference genomes.Conclusions: Two stable and major QTL for KL and KW across six environments were detected and verified in three biparental populations and two natural populations. Significant relationships between kernel size and yield-related traits were identified. KASP markers tightly linked the two major QTL could contribute greatly to subsequent fine mapping. These results suggested the application potential of wheat related species in wheat genetic improvement.

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QTL analysis and fine mapping of a major QTL conferring kernel size in maize (Zea mays)

10.21203/rs.3.rs-20357/v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Guiying Wang ◽

Yanming Zhao ◽

Zhen Zhu ◽

Xinyuan Zhang ◽

Minghua Jiang ◽

...

Keyword(s):

Candidate Gene ◽

Linkage Map ◽

Fine Mapping ◽

Marker Assisted Selection ◽

Chromosome 9 ◽

Recurrent Parent ◽

Kernel Size ◽

Kernel Length ◽

Stable Qtls ◽

Major Qtl

Abstract Background：Kernel size are important agronomic traits for grain yield in maize. The objective of this study is to map QTLs for kernel size, fine map a stable QTL qKL-2 and predict candidate genes for kernel length in maize. A total 199 F2:3 lines were obtained from selfing F2 individuals from the cross SG5/SG7. In this study, a high density genetic linkage map with 3305 bin-markers spanning a total length of 2236.66 cM on 10 chromosomes was applied for primary QTL mapping. Composite interval mapping (CIM) method was used for detecting QTLs in three environments of F2 and F2:3 populations. Results：The result showed that a total ten QTLs for kernel size were detected, among which five QTLs for kernel length (KL) and five QTLs for kernel width (KW). Two stable QTLs qKW-1 and qKL-2 were mapped in all three environments. In order to validate and fine map qKL-2 , near isogenic lines (NILs) were developed by continuous backcross between SG5 as the donor parent and SG7 as the recurrent parent. Marker assisted selection was conducted from BC2F1 generation with molecular markers near qKL-2. Secondary linkage map with six markers around the objective region was developed for fine mapping qKL-2. Finally, qKL-2 was mapped in a 1.95Mb physical interval on maize chromosome 9 by blasting with Zea_Mays_B73 v4 genome. The results were confirmed with selected overlapping recombinant chromosomes. A total 11 out of 40 protein coding genes in the identified interval differentially expressed after conducting transcriptomic analysis between the two parents. GRMZM2G006080, which encodes receptor-like protein kinase FERONIA was predicted as candidate gene to control kernel size. Conclusions：A total ten QTLs for kernel size were identified. Two stable QTLs qKL-2 and qKW-2 were mapped in three envionments. Major QTL qKL-2 for KL was validated and fine mapped in a 1.95Mb physical interval. GRMZM2G006080 was predicted as candidate gene for qKL-2 to control kernel length. The work will not only help to understand the mechanisms that control kernel size of maize, but also provide new gene for marker-assisted selection in further studies.

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Identification of a major QTL on chromosome arm 2AL for reducing yellow rust severity from a Chinese wheat landrace with evidence for durable resistance

Theoretical and Applied Genetics ◽

10.1007/s00122-018-3232-1 ◽

2018 ◽

Vol 132 (2) ◽

pp. 457-471 ◽

Cited By ~ 1

Author(s):

Zhen Wang ◽

Junda Ren ◽

Ziyi Du ◽

Mingzhe Che ◽

Yibin Zhang ◽

...

Keyword(s):

Yellow Rust ◽

Durable Resistance ◽

Wheat Landrace ◽

Chromosome Arm ◽

Rust Severity ◽

Chinese Wheat ◽

Major Qtl

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Association Mapping and Transcriptome Analysis Reveal the Genetic Architecture of Maize Kernel Size

Frontiers in Plant Science ◽

10.3389/fpls.2021.632788 ◽

2021 ◽

Vol 12 ◽

Author(s):

Juan Ma ◽

Lifeng Wang ◽

Yanyong Cao ◽

Hao Wang ◽

Huiyong Li

Keyword(s):

Differential Expression ◽

Genetic Architecture ◽

Genome Wide Association Study ◽

Differential Expression Analysis ◽

Inbred Lines ◽

Kernel Size ◽

Maize Kernel ◽

Association Panel ◽

Kernel Length ◽

A Genome

Kernel length, kernel width, and kernel thickness are important traits affecting grain yield and product quality. Here, the genetic architecture of the three kernel size traits was dissected in an association panel of 309 maize inbred lines using four statistical methods. Forty-two significant single nucleotide polymorphisms (SNPs; p < 1.72E-05) and 70 genes for the three traits were identified under five environments. One and eight SNPs were co-detected in two environments and by at least two methods, respectively, and they explained 5.87–9.59% of the phenotypic variation. Comparing the transcriptomes of two inbred lines with contrasting seed size, three and eight genes identified in the association panel showed significantly differential expression between the two genotypes at 15 and 39 days after pollination, respectively. Ten and 17 genes identified by a genome-wide association study were significantly differentially expressed between the two development stages in the two genotypes. Combining environment−/method-stable SNPs and differential expression analysis, ribosomal protein L7, jasmonate-regulated gene 21, serine/threonine-protein kinase RUNKEL, AP2-EREBP-transcription factor 16, and Zm00001d035222 (cell wall protein IFF6-like) were important candidate genes for maize kernel size and development.

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Molecular mapping of major QTL conferring resistance to orange wheat blossom midge (Sitodiplosis mosellana) in Chinese wheat varieties with selective populations

Theoretical and Applied Genetics ◽

10.1007/s00122-019-03480-4 ◽

2019 ◽

Vol 133 (2) ◽

pp. 491-502 ◽

Cited By ~ 2

Author(s):

Lijing Zhang ◽

Miaomiao Geng ◽

Zhe Zhang ◽

Yue Zhang ◽

Guijun Yan ◽

...

Keyword(s):

Molecular Mapping ◽

Wheat Varieties ◽

Sitodiplosis Mosellana ◽

Chinese Wheat ◽

Major Qtl ◽

Wheat Blossom Midge

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

BMC Genetics ◽

10.1186/s12863-019-0782-4 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 10

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.

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Dichoropetalum schottii: examination of the type specimen, distribution and comparison with D. carvifolium-chabraei (Apiaceae)

Natural History Sciences ◽

10.4081/nhs.2015.255 ◽

2015 ◽

Vol 2 (2) ◽

pp. 131

Author(s):

Eugene V. Kljuykov ◽

Tatiana A. Ostroumova ◽

Fabio Conti ◽

Patricia M. Tilney

Keyword(s):

Related Species ◽

Natural Populations ◽

Type Specimen ◽

Botanical Garden ◽

Secretory Ducts

The lectotype and isolectotype specimens of Peucedanum schottii, based on plants originally cultivated in Cremenets Botanical Garden, have been studied in detail. The geographic provenance of the plants is unknown but they are identical to natural populations in Albania, Bosnia & Herzegovina, Croatia, France, Greece, Italy, Montenegro and Serbia. The valid name for this plant is therefore Dichoropetalum schottii. It differs from a related species, D. carvifolium-chabraei, in having glabrous umbel rays, white (not yellow) petals, long styles and solitary secretory ducts in fruit valleculae.

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Characterization of an incomplete leaf rust resistance gene on chromosome 1RS and development of KASP markers for Lr47 in wheat

Phytopathology ◽

10.1094/phyto-07-20-0308-r ◽

2020 ◽

Author(s):

Xiangyang Xu ◽

Genqiao Li ◽

Guihua Bai ◽

Amy Bernardo ◽

Brett F Carver ◽

...

Keyword(s):

Leaf Rust ◽

Resistance Gene ◽

Great Plains ◽

Rust Resistance ◽

Leaf Rust Resistance ◽

Rust Resistance Gene ◽

Leaf Rust Resistance Gene ◽

Breeding Lines ◽

Chromosome Arm ◽

Kasp Markers

Leaf rust, caused by Puccininia triticina (Pt), is one of the most common wheat diseases in the Great Plains of the USA. A population of recombinant inbred lines (RILs) from CI 17884 x Bainong 418 was evaluated for responses to leaf rust race Pt52-2 and genotyped using single nucleotide polymorphism (SNP) markers. Quantitative trait locus (QTL) analysis identified a minor gene for resistance to leaf rust, designated QLr.stars-1RS, on the 1BL.1RS translocation segment in Bainong 418, and another leaf rust resistance gene, Lr47, on chromosome 7A of CI 17884. Lr47, originally identified in CI 17884 and located in a wheat-T. speltoides translocation segment 7S#1S, remains one of only a few race-specific resistance genes still effective in the Great Plains. A set of 7A-specific simple sequence repeat (SSR) markers were developed and used to genotype CI 17884 and a pair of near-isogenic lines differing in the presence or absence of 7S#1S, PI 603918 and Pavon F76. Haplotype analysis indicated that the estimated length of 7S#1S was 157.23 to 174.42 Mb, accounting for about 23% of the 7A chromosome. Two SNPs on 7S#1S and 4 SNPs on the 1RS chromosome arm were converted to KASP markers, which were subsequently validated in a panel of cultivars and recently released elite breeding lines. Of these, one and two KASP markers are specific to the 1RS chromosome arm and 7S#1S, respectively, indicating that they can facilitate the introgression of Lr47 and QLr.stars-1BS into locally adapted wheat cultivars and breeding lines.

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