Detection of QTLs for important agronomical traits in hexaploid wheat using association analysis

Brbaklić, Ljiljana; Trkulja, Dragana; Kondić‐Špika, Ankica; Treskic, S.; Kobiljski, Borislav

doi:10.17221/64/2012-cjgpb

Cited by 8 publications

(3 citation statements)

References 26 publications

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“…GWAS analysis for BLS resistance was performed with GAPIT (Tang et al, 2016) using 299 hard winter wheat accessions and 15,990 SNPs with MAF >5%. The marker properties, Linkage disequilibrium (LD), principal component (PC) matrix, hierarchical clustering, and Q+K mixed model (Brbaklic et al, 2013) were estimated to account for structure (Q) and kinship (K) in GAPIT. Kinship was estimated using default VanRaden algorithm.…”

Section: Methodsmentioning

confidence: 99%

Molecular characterization of bacterial leaf streak resistance in hard winter wheat

Ramakrishnan

Sidhu

Ali

et al. 2019

PeerJ

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Bacterial leaf streak (BLS) caused by Xanthomonas campestris pv. translucens is one of the major bacterial diseases threatening wheat production in the United States Northern Great Plains (NGP) region. It is a sporadic but widespread wheat disease that can cause significant loss in grain yield and quality. Identification and characterization of genomic regions in wheat that confer resistance to BLS will help track resistance genes/QTLs in future wheat breeding. In this study, we evaluated a hard winter wheat association mapping panel (HWWAMP) containing 299 hard winter wheat lines from the US hard winter wheat growing region for their reactions to BLS. We observed a range of BLS responses among the lines, importantly, we identified ten genotypes that showed a resistant reaction both in greenhouse and field evaluation. Genome-wide association analysis with 15,990 SNPs was conducted using an exponentially compressed mixed linear model. Five genomic regions (p < 0.001) that regulate the resistance to BLS were identified on chromosomes 1AL, 1BS, 3AL, 4AL, and 7AS. The QTLs Q.bls.sdsu-1AL, Q.bls.sdsu-1BS, Q.bls.sdsu-3AL, Q.bls.sdsu-4AL, and Q.bls.sdsu-7AS explain a total of 42% of the variation. In silico analysis of sequences in the candidate regions on chromosomes 1AL, 1BS, 3AL, 4AL, and 7AS identified 10, 25, 22, eight, and nine genes, respectively with known plant defense-related functions. Comparative analysis with rice showed two syntenic regions in rice that harbor genes for bacterial leaf streak resistance. The ten BLS resistant genotypes and SNP markers linked to the QTLs identified in our study could facilitate breeding for BLS resistance in winter wheat.

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Section: Methodsmentioning

confidence: 99%

Molecular characterization of bacterial leaf streak resistance in hard winter wheat

Ramakrishnan

Sidhu

Ali

et al. 2019

PeerJ

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“…Salah satu tujuan utama pemuliaan gandum adalah untuk menentukan daerah genom spesifik yang mengontrol karakter agronomi (Brbaklic L et al 2013). Banyak penelitian yang menggunakan populasi spesifik untuk menganalisis dan menemukan QTL yang bertanggungjawab terhadap ekspresi gen komponen hasil.…”

Section: Pendahuluanunclassified

Seleksi Genotipe Gandum Tropis Toleran Suhu Tinggi Menggunakan Marka SSR

Kadir¹,

Kaimuddin²,

Musa³

et al. 2019

j.ilm.inov.

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High temperature stresses is a challenge for developing the wheat in tropical environments and affect each stage of plant development. Therefore, early detection of yield characteristics using high-temperature linked markers is necessary in order to produce adaptive varieties in tropical environments. The purpose of this study was to detect differences in the formation of band patterns from tropical wheat populations from field selection using SSR markers for heat tolerant. This experiment used 10 selected genotypes and tested with 10 SSR markers for heat tolerant. The results showed that from 10 SSR primers only 2 primers showed a difference in band size, namely on the XGWM285 and XBARC197 primers which were formed only in OHP12a1-1-9 genotypes.Keywords : Tropical wheat, Simple sequence repeat (SSR) marker, heat tolerant, Genotypes

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“…SSRs can be mined and developed from genomic (gSSRs) or expressed sequence tag (e- or EST-SSRs) sequences, each with their own advantages and disadvantages [ 19 , 20 ]. SSR markers in general have been widely used in genetic studies including genetic diversity and population structure [ 21 , 22 , 23 ], constructing genetic maps [ 24 , 25 ], and quantitative trait loci (QTL) mapping [ 26 , 27 ]. Additionally, SSR markers can be used as a quick, low cost tool to identify cultivars, which is useful in breeding programs [ 28 ].…”

Section: Introductionmentioning

confidence: 99%

Development and Characterization of 20 Genomic SSR Markers for Ornamental Cultivars of Weigela

Hamm

Boggess

Kandel³

et al. 2022

Plants

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Weigela (Caprifoliaceae) is a genus of ornamental plants popular for its phenotypic variation and hardiness, that includes species hybridized to produce the commercially available cultivars. Despite its popularity, limited genetic resources exist for the genus. Twenty genomic simple sequence repeat (gSSR) markers distributed across the genome were developed using low coverage whole-genome sequencing data of Weigela Spilled Wine®. A cross-amplification evaluation with these 20 gSSR markers on a collection of 18 Weigela cultivars revealed a total of 111 unique alleles, including 36 private alleles. A diagrammatic key was constructed to identify cultivars using only six of the gSSR markers, demonstrating the newly developed gSSR markers are immediately useful for cultivar identification. Future uses could include breeding with marker-assisted selection, determining the history of hybridization of the current cultivated lines, aiding in the construction of genetic maps, and assessing the patterns of population genetic structure of Weigela spp.

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Detection of QTLs for important agronomical traits in hexaploid wheat using association analysis

Cited by 8 publications

References 26 publications

Molecular characterization of bacterial leaf streak resistance in hard winter wheat

Molecular characterization of bacterial leaf streak resistance in hard winter wheat

Seleksi Genotipe Gandum Tropis Toleran Suhu Tinggi Menggunakan Marka SSR

Development and Characterization of 20 Genomic SSR Markers for Ornamental Cultivars of Weigela

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