Analysis of Structural Genomic Diversity in Aegilops umbellulata, Ae. markgrafii, Ae. comosa, and Ae. uniaristata by Fluorescence In Situ Hybridization Karyotyping

Song, Zhongping; Dai, Shoufen; Bao, Tingyu; Zuo, Ya‐Gang; Qin, Xiang; Li, Jian; Liu, Gang; Yan, Zehong

doi:10.3389/fpls.2020.00710

Cited by 21 publications

(24 citation statements)

References 80 publications

(119 reference statements)

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“…Four oligonucleotide probes, namely Oligo-pSc119.2-1 (pSc119.2), Oligo-pTa535-1 (pTa-535), Oligo-pTa71-2 (pTa71) (Tang et al 2014), and (CTT) 12 (Song et al 2020), were used for FISH analysis. These probes were synthesized by Tsingke in Chengdu, China.…”

Section: Cytological Observation and Fish Analysismentioning

confidence: 99%

“…The polymorphism of FISH signals among 48 Ae. comosa accessions were discovered using probes pSc119.2, (CTT) 12 and pTa 71, which allowed precise identi cation of M chromosomes from different accessions (Song et al 2020). Single nucleotide polymorphisms (SNPs) are one of the most abundant molecular markers in plant (Lai et al 2012;Cui et al 2017).…”

Section: Introductionmentioning

confidence: 99%

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Identification and Characterization of Wheat - Aegilops Comosa 7M/7A Disomic Substitution Lines with Stripe Rust Resistance

Zuo¹,

Dai²,

Song³

et al. 2021

Preprint

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Aegilops comosa (MM, 2n = 2x = 14), an important diploid species belonging to wheat tertiary gene pools, contains many excellent genes/traits, including disease resistance for wheat breeding. In this study, three sister lines, NAL-32, NAL-33, and NAL-34, were identified from a wheat - Ae. comosa distant cross using fluorescence in situ hybridization (FISH) combined with single nucleotide polymorphism (SNP) microarray analysis. Genetically, NAL-32 contained neither an alien nor translocation chromosome, whereas NAL-33 and NAL-34 had disomic 7M/7A substitution chromosomes but differed in the absence (NAL-33) or presence (NAL-34) of 1BL/1RS translocation chromosomes. The substitution of 7M/7A in NAL-33 and NAL-34 was verified using wheat 55 K SNP arrays but 1BL/1RS translocation in NAL-34 was not. The two 7M/7A substitution lines, NAL-33 and NAL-34, had similar stripe rust resistance, and both showed higher stripe rust resistance than NAL-32 and their parents, suggesting that stripe rust resistance in NAL-33 and NAL-34 was derived from the 7M of Ae. comosa and that their resistance was likely irrelevant to 1BL/1RS translocation. Meanwhile, the three NAL lines also showed higher grain weights (grams per 50 grains) than one to three of their three wheat parents, and the two 7M/7A substitution lines, NAL-33 and NAL-34, had larger seed size-related traits than NAL-32, suggesting that both the 7M and 1BL/1RS chromosomes had positive effects on seed size-related traits. The results provide important bridge materials that can potentially be used for transferring stripe rust resistance, as well as seed size-related traits from Ae. comosa to wheat.

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Section: Cytological Observation and Fish Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification and Characterization of Wheat - Aegilops Comosa 7M/7A Disomic Substitution Lines with Stripe Rust Resistance

Zuo¹,

Dai²,

Song³

et al. 2021

Preprint

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“…Fluorescent in situ hybridization (FISH) is a powerful molecular cytogenetic technique to characterize karyotype variation at chromosome level by direct localization of repetitive DNA sequences on plant chromosomes ( Jiang and Gill, 2006 ; Patokar et al, 2016 ; Song et al, 2020 ), enabling identification of chromosomes even in species with small and morphologically indistinguishable chromosomes, and comparison of chromosomal organization between species. However, such probes can be inconsistent in chromosome identification for multiplicity of repeat sequences and variations in their genomic locations ( Mukai et al, 1993 ; Fransz et al, 1998 ; Kato et al, 2004 ; Danilova et al, 2012 ; Komuro et al, 2013 ; Koo et al, 2016 ; Amosova et al, 2017 ; Krivankova et al, 2017 ; Hou et al, 2018 ; Said et al, 2018 ), and repetitive DNA sequences with suitable genomic locations may not exist.…”

Section: Introductionmentioning

confidence: 99%

Identification of Chromosomes and Chromosome Rearrangements in Crop Brassicas and Raphanus sativus: A Cytogenetic Toolkit Using Synthesized Massive Oligonucleotide Libraries

et al. 2020

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Crop brassicas include three diploid [Brassica rapa (AA; 2n = 2x = 16), B. nigra (BB; 2n = 2x = 18), and B. oleracea (CC; 2n = 2x = 20)] and three derived allotetraploid species. It is difficult to distinguish Brassica chromosomes as they are small and morphologically similar. We aimed to develop a genome-sequence based cytogenetic toolkit for reproducible identification of Brassica chromosomes and their structural variations. A bioinformatic pipeline was used to extract repeat-free sequences from the whole genome assembly of B. rapa. Identified sequences were subsequently used to develop four c. 47-mer oligonucleotide libraries comprising 27,100, 11,084, 9,291, and 16,312 oligonucleotides. We selected these oligonucleotides after removing repeats from 18 identified sites (500–1,000 kb) with 1,997–5,420 oligonucleotides localized at each site in B. rapa. For one set of probes, a new method for amplification or immortalization of the library is described. oligonucleotide probes produced specific and reproducible in situ hybridization patterns for all chromosomes belonging to A, B, C, and R (Raphanus sativus) genomes. The probes were able to identify structural changes between the genomes, including translocations, fusions, and deletions. Furthermore, the probes were able to identify a structural translocation between a pak choi and turnip cultivar of B. rapa. Overall, the comparative chromosomal mapping helps understand the role of chromosome structural changes during genome evolution and speciation in the family Brassicaceae. The probes can also be used to identify chromosomes in aneuploids such as addition lines used for gene mapping, and to track transfer of chromosomes in hybridization and breeding programs.

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“…Up to now, several wheat-Ae. biuncialis disomic addition lines have been developed carrying the chromosomes 1U, 3U, 6U, 2M, 3M, 5M and 7M besides the whole wheat genome, respectively [30][31][32] . In addition, a 3M.4BS translocation line possessing the 3M chromosome arm from Ae.…”

mentioning

confidence: 99%

Addition of Aegilops biuncialis chromosomes 2M or 3M improves the salt tolerance of wheat in different way

Darkó

Khalil

Dobi

et al. 2020

Sci Rep

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Aegilops biuncialis is a promising gene source to improve salt tolerance of wheat via interspecific hybridization. In the present work, the salt stress responses of wheat-Ae. biuncialis addition lines were investigated during germination and in young plants to identify which Aegilops chromosomes can improve the salt tolerance of wheat. After salt treatments, the Aegilops parent and the addition lines 2M, 3M and 3M.4BS showed higher germination potential, shoot and root growth, better CO2 assimilation capacity and less chlorophyll degradation than the wheat parent. The Aegilops parent accumulated less Na in the roots due to an up-regulation of SOS1, SOS2 and HVP1 genes, while it contained higher amount of proline, fructose, glucose, galactose, maltose and raffinose. In the leaves, lower Na level was accompanied by high amount of proline and increased expression of NHX2 gene. The enhanced accumulation of sugars and proline was also observed in the roots of 3M and 3M.4BS addition lines. Typical mechanism of 2M addition line was the sequestration of Na into the vacuole due to the increased expression of HVP1 in the roots and NHX2 in the leaves. These results suggest the Aegilops chromosomes 2M and 3M can improve salt tolerance of wheat in different way.

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Analysis of Structural Genomic Diversity in Aegilops umbellulata, Ae. markgrafii, Ae. comosa, and Ae. uniaristata by Fluorescence In Situ Hybridization Karyotyping

Cited by 21 publications

References 80 publications

Identification and Characterization of Wheat - Aegilops Comosa 7M/7A Disomic Substitution Lines with Stripe Rust Resistance

Identification and Characterization of Wheat - Aegilops Comosa 7M/7A Disomic Substitution Lines with Stripe Rust Resistance

Identification of Chromosomes and Chromosome Rearrangements in Crop Brassicas and Raphanus sativus: A Cytogenetic Toolkit Using Synthesized Massive Oligonucleotide Libraries

Addition of Aegilops biuncialis chromosomes 2M or 3M improves the salt tolerance of wheat in different way

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