“…6a ). Knowing the relative expression levels of different gene copies can be useful when conducting targeted downregulation of enzymes for forage quality improvement by reducing lignin content, for example 36 , 38 , 39 . Fig.…”
Section: Resultsmentioning
confidence: 99%
“…We further identified 82 and 85 candidate genes that may be involved in the lignin and cellulose biosynthesis pathways, respectively, and described the expression profiles of these genes in leaf and stem tissues. Such information will be very useful for improving alfalfa quality in the future, for example, by the downregulation of targeted enzymes 36 , 38 , 39 or through gene editing to decrease lignin content. The available genome sequence for the direct progenitor of autotetraploid alfalfa is an important complement to the alfalfa genome and holds great promise for further understanding fundamental aspects of genomic architecture and improving molecular breeding strategies in alfalfa.…”
Alfalfa (Medicago sativa L.) is one of the most important and widely cultivated forage crops. It is commonly used as a vegetable and medicinal herb because of its excellent nutritional quality and significant economic value. Based on Illumina, Nanopore and Hi-C data, we assembled a chromosome-scale assembly of Medicago sativa spp. caerulea (voucher PI464715), the direct diploid progenitor of autotetraploid alfalfa. The assembled genome comprises 793.2 Mb of genomic sequence and 47,202 annotated protein-coding genes. The contig N50 length is 3.86 Mb. This genome is almost twofold larger and contains more annotated protein-coding genes than that of its close relative, Medicago truncatula (420 Mb and 44,623 genes). The more expanded gene families compared with those in M. truncatula and the expansion of repetitive elements rather than whole-genome duplication (i.e., the two species share the ancestral Papilionoideae whole-genome duplication event) may have contributed to the large genome size of M. sativa spp. caerulea. Comparative and evolutionary analyses revealed that M. sativa spp. caerulea diverged from M. truncatula ~5.2 million years ago, and the chromosomal fissions and fusions detected between the two genomes occurred during the divergence of the two species. In addition, we identified 489 resistance (R) genes and 82 and 85 candidate genes involved in the lignin and cellulose biosynthesis pathways, respectively. The near-complete and accurate diploid alfalfa reference genome obtained herein serves as an important complement to the recently assembled autotetraploid alfalfa genome and will provide valuable genomic resources for investigating the genomic architecture of autotetraploid alfalfa as well as for improving breeding strategies in alfalfa.
“…6a ). Knowing the relative expression levels of different gene copies can be useful when conducting targeted downregulation of enzymes for forage quality improvement by reducing lignin content, for example 36 , 38 , 39 . Fig.…”
Section: Resultsmentioning
confidence: 99%
“…We further identified 82 and 85 candidate genes that may be involved in the lignin and cellulose biosynthesis pathways, respectively, and described the expression profiles of these genes in leaf and stem tissues. Such information will be very useful for improving alfalfa quality in the future, for example, by the downregulation of targeted enzymes 36 , 38 , 39 or through gene editing to decrease lignin content. The available genome sequence for the direct progenitor of autotetraploid alfalfa is an important complement to the alfalfa genome and holds great promise for further understanding fundamental aspects of genomic architecture and improving molecular breeding strategies in alfalfa.…”
Alfalfa (Medicago sativa L.) is one of the most important and widely cultivated forage crops. It is commonly used as a vegetable and medicinal herb because of its excellent nutritional quality and significant economic value. Based on Illumina, Nanopore and Hi-C data, we assembled a chromosome-scale assembly of Medicago sativa spp. caerulea (voucher PI464715), the direct diploid progenitor of autotetraploid alfalfa. The assembled genome comprises 793.2 Mb of genomic sequence and 47,202 annotated protein-coding genes. The contig N50 length is 3.86 Mb. This genome is almost twofold larger and contains more annotated protein-coding genes than that of its close relative, Medicago truncatula (420 Mb and 44,623 genes). The more expanded gene families compared with those in M. truncatula and the expansion of repetitive elements rather than whole-genome duplication (i.e., the two species share the ancestral Papilionoideae whole-genome duplication event) may have contributed to the large genome size of M. sativa spp. caerulea. Comparative and evolutionary analyses revealed that M. sativa spp. caerulea diverged from M. truncatula ~5.2 million years ago, and the chromosomal fissions and fusions detected between the two genomes occurred during the divergence of the two species. In addition, we identified 489 resistance (R) genes and 82 and 85 candidate genes involved in the lignin and cellulose biosynthesis pathways, respectively. The near-complete and accurate diploid alfalfa reference genome obtained herein serves as an important complement to the recently assembled autotetraploid alfalfa genome and will provide valuable genomic resources for investigating the genomic architecture of autotetraploid alfalfa as well as for improving breeding strategies in alfalfa.
“…The aboveground biomass was harvested manually at 5‐cm stubble height four times—on 15 May, 13 June, 14 July, and 17 Aug, 2017—to determine fresh biomass (kg) per plot onsite as previously described (Bhattarai et al, 2018), using an Ohaus Defender 3000 scale (Parsippany, NJ) connected directly to a rugged tablet (Panasonic Toughpad). Samples placed inside labeled paper bags were dried inside forced‐air ovens at 63°C for 2 d to determine shoot dry biomass.…”
Section: Methodsmentioning
confidence: 99%
“…Seedling plant growth was cut back to the third node on 3 Oct. 2016 to minimize variations associated with differences in seedling emergence and vigor. The experimental design was a randomized complete block with four replications and 10 individuals per replication for a total of 40 plants evaluated per accession as previously described for alfalfa spaced plants (Bhattarai et al, 2018). All plants were transplanted to the field site on 18 Oct. 2016.…”
Remote sensing technologies enable rapid and nondestructive phenotyping of plants in the field.
Biomass estimate accuracy from images and sensors was similar to yields harvested manually.
Biomass yield variation identified the most productive accessions under low‐input conditions.
High‐throughput phenotyping technologies enable monitoring plant growth and development nondestructively throughout the growing season. Crop losses associated with abiotic and biotic factors threaten the sustainability of crops used for feed, fiber, and fuel. The process to develop improved cultivars with enhanced crop yields includes phenotyping hundreds of plants under a target set of conditions. However, the manual collection of data is often laborious and time consuming. Strategies that integrate remote sensing technologies including unmanned aerial vehicles (UAVs) and sensors mounted on “phenomobiles” can streamline phenotyping efforts in plant breeding programs. The objectives of this study were to compare the phenotypic data collected from the field using UAVs, sensors, and manual approaches and to assess the potential of high‐throughput approaches to rank the productivity of alfalfa (Medicago sativa L.) accessions growing in the field. Phenotypic data were collected from 100 alfalfa accessions established and grown under low‐input conditions. Specific traits evaluated using both UAVs and sensors mounted on a phenomobile prior to physically harvesting the biomass during four harvests include biomass yield, plant height, normalized difference vegetation index, leaf area index, and ground coverage. The results from both the UAV and the sensors were highly correlated to the physical measurements obtained for the multiple traits evaluated. Therefore, field‐based high‐throughput phenotyping strategies represent a viable option for efficiently screening germplasm in the field to increase phenotyping efficiencies in plant breeding programs.
“…In order to better understand the precise physiological roles of HCT and HQT in vivo , various studies were undertaken using mutational, down-regulation, RNA i , and/or overexpression strategies. ,,− However, none of these studies comprehensively examined effects on both CGA ( 1 ) and lignin levels together. This is an important issue to consider, since gene redundancy and metabolic cross-talk can be very important in many biochemical pathways, including phenylpropanoid metabolism.…”
Chlorogenic acid (CGA) and guaiacyl/syringyl (G/ S) lignin formation involves hydroxycinnamoyl ester intermediacy, the latter formed via hydroxycinnamoyl CoA:shikimate hydroxycinnamoyl transferase (HCT) and hydroxycinnamoyl CoA:quinate hydroxycinnamoyl transferase (HQT) activities. HQT and HCT RNAi silencing of a commercial tobacco (Nicotiana tabacum) K326 line was examined herein. NtHQT gene silencing gave relatively normal plant phenotypes, with CGA levels reduced (down to 1% of wild type) with no effects on lignin. RNAi NtHCT silencing had markedly adverse phenotypes (e.g., stunted, multiple stems, delayed flowering, with senescence delayed by several months). Lignin contents were partially lowered, with a small increase in cleavable p-hydroxyphenyl (H) monomers; those plants had no detectable CGA level differences relative to wild type. In vitro NtHCT kinetic parameters revealed preferential p-coumaroyl CoA and shikimate esterification, as compared to other structurally related potential acyl group donors and acceptors. In the presence of coenzyme A, NtHCT catalyzed the reverse reaction. Site-directed mutagenesis of NtHCT (His153Ala) abolished enzymatic activity. NtHQT, by comparison, catalyzed preferential conversion of p-coumaroyl CoA and quinic acid to form pcoumaroyl quinate, the presumed CGA precursor. In sum, metabolic pathways to CGA and lignins appear to be fully independent, and previous conflicting reports of substrate versatilities and metabolic cross-talk are resolved.
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