Identification of peanut (<i>Arachis hypogaea)</i> chromosomes using a fluorescence <i>in situ</i> hybridization system reveals multiple hybridization events during tetraploid peanut formation

Zhang, Laining; Yang, Xiaoyu; Tian, Li; Chen, Lei; Yu, Weichang

doi:10.1111/nph.13999

Cited by 33 publications

(39 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Peaks in LTR retrotransposons are footprints of these insertion events, demonstrating a major burst of amplification in all four genome sets around 1-2 Mya, and revealing an additional burst only in the A t subgenome, which contributed to a larger genome size than that of the suspected progenitor ( Figure 4C). Strikingly, this A t -specific activation of TEs occurred around $0.2 Mya before/during allopolyploid formation, indicating that the two subgenomes independently asymmetrically evolved, implying the possibility of another wild A-genome diploid as the donor for the A t subgenome of A. hypogaea, or multiple hybridization events of the B progenitor, A. ipaensis, with different varieties of A. duranensis, to form the present-day cultivated peanut (Zhang et al, 2016). Asymmetric evolution was also reflected by the genomic signature of selection; there were 694 positively selected genes (PSGs), with significantly more PSGs in the A t subgenome (395 PSGs) than in the B t subgenome (299 PSGs, P < 0.01, Fisher's exact test; Figure 4D).…”

Section: Asymmetric Evolution Of the Two Subgenomes Of A Hypogaeamentioning

confidence: 99%

Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement

et al. 2019

View full text Add to dashboard Cite

Background B-box (BBX) proteins are important factors involving in the regulation of plant growth and development, and have been identified in many plant species. However, the characteristics and transcription patterns of BBX genes in wild peanut are limited. Results In the present study, we identified and characterized 24 BBX genes in a wild peanut Arachis duranensis. The AdBBX members distributed on 9 of the 10 chromosomes and chromosome 3 contained the most AdBBX members, with 6 AdBBXs. 16 AdBBX proteins had two distinct BBX domains, 11 members contained one CCT domain, and 7 genes had both BBX and CCT domains. Protein structure analysis revealed that AdBBX were classified into five clades: I (3 genes), II (4 genes), III (4 genes), IV (9 genes) and V (4 genes), on the basis of the diversity of conserved BBX and CCT domains. Moreover, 15 distinct motifs were found in these 24 AdBBX proteins and motif 1 and 5 existed in all the AdBBX proteins. Duplication analysis revealed that 4 interchromosomal duplicated gene pairs were obtained and all of them belonged to group IV. In addition, 95 kinds of cis-acting elements were found in the promoter regions of AdBBXs and 53 types were predicted to have putative functions. The numbers and types of cis-acting elements varied in these AdBBX promoters, as a result, AdBBX genes exhibited distinct expression levels in different tissues. The transcription investigation combined with synteny analysis suggested AdBBX8 might be the key factor involving in flowering time regulation in Arachis duranensis. Conclusion Overall, this study provides a genome-wide identification of BBX genes in a wild peanut Arachis duranensis. Characteristic and transcription pattern analysis revealed their critical roles in plant growth and development. Our study will provide essential information for further functional characteristic investigation of AdBBX genes.

show abstract

Section: Asymmetric Evolution Of the Two Subgenomes Of A Hypogaeamentioning

confidence: 99%

Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement

et al. 2019

View full text Add to dashboard Cite

show abstract

“…Telomeric and centromeric repeat probes were used to investigate the evolutionary relationship among cultivated peanut and wild species. Multiple hybridization events reportedly occur during tetraploid peanut formation [23]. Four repetitive oligo probes capable of staining the chromosomes of 51 Arachis species con rmed the relationships among the A, B, K, F, E, and H genomes [32].…”

Section: Applications Of the New Oligo Probesmentioning

confidence: 79%

“…Both C-banding [19] and uorescent in situ hybridization banding [20] can effectively identify chromosomal structural variants. Although 5S and 45S rDNA [21], telomeres [22], and bacterial arti cial chromosome (BAC) probes [23] have been developed in peanut, the cytogenetic markers in chromosomal identi cation is still very insu cient. Furthermore, the preparation of these markers is time-consuming and expensive.…”

Section: Introductionmentioning

confidence: 99%

Development of a karyotype associated with the genome map and its applications in identification and characterization of chromosomes in peanut

Wang

et al. 2020

Preprint

View full text Add to dashboard Cite

Abstract Background Chromosomal structural variants are important materials for crop breeding and genetic research. Oligo fluorescence in situ hybridization (oligo FISH) is a useful tool for the identification of chromosomal structural variants. Results We developed 114 new repetitive oligos based on genome-wide tandem repeats (TRs) using genomic reference sequences of the cultivar Tifrunner and the diploid species Arachis ipaensis by bioinformatics and FISH. These oligo probes were positioned and classified into 28 types. Signals produced by representative probes from eight types were in the secondary constriction, middle arm, and terminal regions; signals of four probe types were on the B subgenome; and one probe being able to produce signals on only one pair of chromosomes could be used to recognize a special genome or chromosomes of peanut. Based on new and previous oligo probes, we developed a cocktail Multiplex #3 including FAM modified TIF-439, TIF-185-1, TIF-134-3, TIF-165-3, and TAMRA modified Ipa-1162, Ipa-1137, DP-1, and DP-5, which combined with the total genomic DNA of A. duranensis and A. ipaensis probes, and 45S rDNA and 5S rDNA probes to establish a karyotype associated with the genome map of peanut and identify 14 chromosomal structural variants. Conclusions The new oligo probes are useful and convenient for distinguishing peanut chromosomes or specific segments of peanut chromosomes. Comparisons of oligo sites in the karyotype and chromosome plots of electronic location revealed the characteristics of repeated sequences, and showed that the assembly of repeated sequence in peanut genomic reference sequence was incomplete. We therefor demonstrated the great potentials of the new oligo probes in facilitating chromosome identification and characterization, and provided novel materials for further study and genetic improvement of peanut.

show abstract

“…However, variations exist between Arachis du-Arachis duranensis varieties from different geographic regions reveal both numeric and positional variations of ITRs in their chromosomes, which are similar to the variations in tetraploid peanut varieties. These results provide evidence for the origin of cultivated peanut from the two diploid ancestors, and suggest that multiple hybridization events of Arachis ipaënsis with different varieties of Arachis duranensis may have occurred during the evolution of cultivated peanut (Figure 1) [1] [2]. The multiple hybridization hypothesis has also been partially supported by the results of genome sequencing for cultivated peanut and the two putative progenitors [3] [4] [5] [6].…”

Section: Introductionmentioning

confidence: 77%

Recent Advances in the Acclimation Mechanisms and Genetic Improvement of Peanut for Drought Tolerance

Yang¹,

Luo²,

Yu³

et al. 2019

Self Cite

View full text Add to dashboard Cite

Peanut (Arachis hypogaea L.) is one of the most important oilseed crops that are cultivated worldwide. Peanut production is now greatly limited by drought stress, which is a major environmental challenge. The urgent task for current peanut research is thus to study the underlying mechanisms of peanut drought tolerance, to identify genes that are closely associated with drought tolerance, and to create new germplasms/varieties with high drought tolerance. In this review, we summarize recent advances in the acclimation mechanisms to water deficiency and the genetic improvement of peanut for drought tolerance, and propose the perspectives for the future peanut research.

show abstract

Identification of peanut (Arachis hypogaea) chromosomes using a fluorescence in situ hybridization system reveals multiple hybridization events during tetraploid peanut formation

Cited by 33 publications

References 53 publications

Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement

Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement

Development of a karyotype associated with the genome map and its applications in identification and characterization of chromosomes in peanut

Recent Advances in the Acclimation Mechanisms and Genetic Improvement of Peanut for Drought Tolerance

Contact Info

Product

Resources

About