scholarly journals Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species

2022 ◽  
Author(s):  
Derek M Bickhart ◽  
Lisa M Koch ◽  
Timothy P.L. Smith ◽  
Heathcliffe Riday ◽  
Michael L Sullivan
Keyword(s):  
Trifolium Pratense ◽  
Red Clover ◽  
Crop Species ◽  
Forage Crop ◽  
Short Read ◽  
Long Read ◽  
Trifolium Pratense L ◽  
Heterozygous Plant ◽  
Modern Genomic ◽  
Genome Assemblies

Red clover (Trifolium pratense L.) is used as a forage crop due to a variety of favorable traits relative to other crops. Improved varieties have been developed through conventional breeding approaches, but progress could be accelerated and gene discovery facilitated using modern genomic methods. Existing short-read based genome assemblies of the ~420 Megabase (Mb) genome are fragmented into >135,000 contigs with numerous errors in order and orientation within scaffolds, likely due to the biology of the plant which displays gametophytic self-incompatibility resulting in inherent high heterozygosity. A high-quality long-read based assembly of red clover is presented that reduces the number of contigs by more than 500-fold, improves the per-base quality, and increases the contig N50 statistic by three orders of magnitude. The 413.5 Mb assembly is nearly 20% longer than the 350 Mb short read assembly, closer to the predicted genome size. Quality measures are presented and full-length isoform sequence of RNA transcripts reported for use in assessing accuracy and for future annotation of the genome. The assembly accurately represents the seven main linkage groups present in the genome of an allogamous (outcrossing), highly heterozygous plant species.

scholarly journals Unveiling the Complexity of Red Clover (Trifolium pratense L.) Transcriptome and Transcriptional Regulation of Isoflavonoid Biosynthesis Using Integrated Long- and Short-Read RNAseq

2021 ◽  
Vol 22 (23) ◽  
pp. 12625
Author(s):  
Kun Shi ◽  
Xiqiang Liu ◽  
Xinyi Pan ◽  
Jia Liu ◽  
Wenlong Gong ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Trifolium Pratense ◽  
Red Clover ◽  
Short Read ◽  
Long Read ◽  
Long Time ◽  
Alternatively Spliced ◽  
Trifolium Pratense L ◽  
High Level

Red clover (Trifolium pratense L.) is used as forage and contains a high level of isoflavonoids. Although isoflavonoids in red clover were discovered a long time ago, the transcriptional regulation of isoflavonoid biosynthesis is virtually unknown because of the lack of accurate and comprehensive characterization of the transcriptome. Here, we used a combination of long-read (PacBio Iso-Seq) and short-read (Illumina) RNAseq sequencing to develop a more comprehensive full-length transcriptome in four tissues (root, stem, leaf, and flower) and to identify transcription factors possibly involved in isoflavonoid biosynthesis in red clover. Overall, we obtained 50,922 isoforms, including 19,860 known genes and 2817 novel isoforms based on the annotation of RefGen Tp_v2.0. We also found 1843 long non-coding RNAs, 1625 fusion genes, and 34,612 alternatively spliced events, with some transcript isoforms validated experimentally. A total of 16,734 differentially expressed genes were identified in the four tissues, including 43 isoflavonoid-biosynthesis-related genes, such as stem-specific expressed TpPAL, TpC4H, and Tp4CL and root-specific expressed TpCHS, TpCHI1, and TpIFS. Further, weighted gene co-expression network analysis and a targeted compound assay were combined to investigate the association between the isoflavonoid content and the transcription factors expression in the four tissues. Twelve transcription factors were identified as key genes for isoflavonoid biosynthesis. Among these transcription factors, the overexpression of TpMYB30 or TpRSM1-2 significantly increased the isoflavonoid content in tobacco. In particular, the glycitin was increased by 50–100 times in the plants overexpressing TpRSM1-2, in comparison to that in the WT plants. Our study provides a comprehensive and accurate annotation of the red clover transcriptome and candidate genes to improve isoflavonoid biosynthesis and accelerate research into molecular breeding in red clover or other crops.

scholarly journals Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

2018 ◽  
Vol 18 (1) ◽  
Author(s):  
Yuehui Chao ◽  
Jianbo Yuan ◽  
Sifeng Li ◽  
Siqiao Jia ◽  
Liebao Han ◽  
...  
Keyword(s):  
Single Molecule ◽  
Trifolium Pratense ◽  
Red Clover ◽  
Splice Isoforms ◽  
Long Read ◽  
Trifolium Pratense L

scholarly journals Red clover grown in a mixture with grasses : yield, persistence and dynamics of quality characteristics

2003 ◽  
Vol 12 (3-4) ◽  
pp. 195-212 ◽  
Author(s):  
T. MELA
Keyword(s):  
Field Experiments ◽  
Trifolium Pratense ◽  
Red Clover ◽  
Forage Yield ◽  
Crude Fibre ◽  
Meadow Fescue ◽  
Forage Crop ◽  
Trifolium Pratense L ◽  
Yield Quality ◽  
Accumulated Temperature

Red clover (Trifolium pratense L.) was grown in mixtures with timothy and meadow fescue in field experiments at four sites in Finland to broaden knowledge on its potential as a forage crop. The effects of cutting frequency, nitrogen fertilization in the spring and sward density were investigated. Forage yield quality was analyzed using standard methods. Red clover produced well in all swards during the two first seasons. In the third summer the proportion of red clover was greatly diminished except on sandy soil at the northernmost locality (64°40'N) where it remained productive. Linear regression adequately described the dependence of crude fibre content and crude protein content in dry matter of the primary growth and regrowth, both of red clover and grass, on accumulated temperature sum. The contents of P, K, Ca and Mg in clover and grass are given as a function of accumulated temperature to describe their changes during crop growth. The results give new knowledge about possibilities to grow red clover in the northern livestock region of Finland. They proved that soil type is more important for good persistence of red clover than latitude.

Comparisons of Floral Response of Seed Lots of Dollard Red Clover, Trifolium pratense L. 1

Crop Science ◽  
1965 ◽  
Vol 5 (5) ◽  
pp. 425-428 ◽  
Author(s):  
R. J. Bula ◽  
R. G. May ◽  
C. S. Garrison ◽  
C. M. Rincker ◽  
J. G. Dean
Keyword(s):  
Trifolium Pratense ◽  
Red Clover ◽  
Trifolium Pratense L

scholarly journals Precrop Effect of Red Clover (Trifolium pratense L.) and Alfalfa (Medicago sativa L.) on the Population Development of the Northern Root-Knot Nematode Meloidogyne hapla Chitwood, 1949 and on Succeeding Crops—A Pot Study

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 722
Author(s):  
Renata Dobosz ◽  
Roman Krawczyk
Keyword(s):  
Population Density ◽  
Medicago Sativa ◽  
Trifolium Pratense ◽  
Red Clover ◽  
Continuous Cultivation ◽  
Nematode Population ◽  
Meloidogyne Hapla ◽  
Root Knot Nematode ◽  
Crop Species ◽  
Tomato Growth

The northern root-knot nematode, Meloidogyne hapla, is a major pest of many crop species. The objective of the study was to determine how M. hapla population dynamics is affected by two precrops, i.e., Trifolium pratense and Medicago sativa, in three crop durations: one, two and three years of continuous cultivation. Moreover, we set ourselves the task of evaluating the effect of the legume precrop soil on the growth of the succeeding tomato plant (Solanum lycopersicum) and on the nematode population. The experiment was performed outdoors in pots with naturally infected soil. Both precrop species investigated were found to modify the J2 nematode population density in the soil. The galls and nematode females with egg masses were observed on the roots of both studied plant species at the end of each growing season. They appeared to be more abundant on the red clover roots than on those of the alfalfa. The obtained data indicate that the spring soil sampling is more appropriate for the estimation of the M. hapla population density in the red clover precrop soil. The legume precrop soil had a limiting effect on tomato growth and fruit yield. The nematode population negatively influenced tomato growth. The experiment revealed that tomato plants could be planted in alfalfa precrop soil following at least three years of continuous alfalfa cultivation. The same cannot be said of the cultivation of red clover as a precrop for tomatoes.

scholarly journals Volatile Constituents of Trifolium Pratense and T. Repens from N.E. Italian Alpine Pastures

2009 ◽  
Vol 4 (6) ◽  
pp. 1934578X0900400 ◽  
Author(s):  
Aldo Tava ◽  
Daniele Ramella ◽  
Maris Grecchi ◽  
Paolo Aceto ◽  
Renato Paoletti ◽  
...  
Keyword(s):  
Steam Distillation ◽  
Trifolium Pratense ◽  
Red Clover ◽  
Volatile Oil ◽  
Volatile Fraction ◽  
Fresh Weight ◽  
Fresh Weight Basis ◽  
Qualitative And Quantitative ◽  
Aerial Parts ◽  
Trifolium Pratense L

The composition of the volatile fraction of two important forage legumes from Italian sub-alpine N.E. pastureland, namely Trifolium pratense L. subsp. pratense (red clover) and T. repens subsp. repens (white clover) were investigated. The volatile oil was obtained from the fresh aerial parts by steam distillation and analyzed by GC/FID and GC/MS. The oil yield was 0.018 and 0.021% (weight/fresh weight basis) for T. pratense and T. repens, respectively. Several classes of compounds were found in both the oils, including alcohols, aldehydes, ketones, terpenes, esters, hydrocarbons, phenolics and acids. Qualitative and quantitative differences were found.

Polycross‐Progeny Testing of Red Clover (trifolium pratense L. 1

Crop Science ◽  
1968 ◽  
Vol 8 (4) ◽  
pp. 451-454 ◽  
Author(s):  
Norman L. Taylor ◽  
W. A. Kendall ◽  
W. H. Stroube
Keyword(s):  
Trifolium Pratense ◽  
Red Clover ◽  
Progeny Testing ◽  
Trifolium Pratense L
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