The 75th percentile varied widely by commodity: $6,172 for those primarily employed by FLCs, $10,572 for those in grapes and $29,465 for those in mushrooms.The number of individuals and jobs reported by agricultural employers increased in the 1990s, reflecting increased production of labor-intensive fruit and vegetable crops and, the data suggests, more farm workers each worked a fewer number of hours. With the state’s minimum wage at $6.25 per hour after Jan. 1, 2001 , the earnings reported by employers suggest that most farm workers are employed fewer than 1,000 hours per year . FLCs increased their market share in the 1990s, but dependence on them varied by commodity. For example, FLCs rather than citrus growers reported many citrus workers, while dairy employers reported most dairy workers. FLCs are associated with low earnings, which suggests few hours of work — the median earnings reported by FLCs for their employees in 2001 were $2,650, or 400 hours if workers earned the state’s $6.25 minimum wage. California’s farm labor market has large numbers of workers searching for seasonal jobs; FLCs are matching an increasing share of these workers with jobs, resulting in lower earnings for FLC employees.If FLCs are most likely to hire recently arrived and unauthorized workers,black plastic plant pots bulk as the National Agricultural Worker Survey suggests, FLCs serve as a port of entry for immigrant farm workers.
The impact of guest workers, legalization and earned legalization will depend on the details of any new program. If the status quo continues, the percentage of unauthorized workers is likely to rise. Alternatively, if there were a legalization program, farm workers might more quickly exit the farm workforce. However, an earned legalization program could slow this exit if workers were required to continue working in agriculture to earn full legal status. The next step in this analysis is to examine the mobility of individual farm workers over time and geography, examining where workers migrate during 1 year and patterns of entrance to and exit from the farm workforce . Do farm workers who increase their earnings by moving to non-farm jobs stay in non-farm jobs, or do they sometimes return to agriculture? Are geographic and economic mobility linked for workers who get non-farm jobs? Answers to these questions will help to determine the trajectory of the farm labor market.In addition to its historical roles in paper production and as ornamentals, varieties of the wild grass Miscanthus can produce high yields of harvestable vegetative biomass while maintaining and potentially increasing soil carbon. These features, enabled by C4 photosynthesis, perenniality, and related high efficiencies of light, nutrient, and water use, make Miscanthus and its close relatives promising candidates for economically feasible and sustainable bio-energy crops. Continued genetic improvement of bio-energy feed stocks is needed to enhance productivity and ensure that these crops remain robust in the face of ongoing biotic and abiotic stresses.
This is particularly true for perennial grasses, where the advantages in economic and environmental sustainability relative to annuals depend on the longevity of the crop once established. Although perennial crops have tremendous potential for maximizing agricultural yields and minimizing environmental impacts, our knowledge of their biology and ability to manipulate their genetics lags well behind that in annual crops. Polyploidy is also common within the Saccharum complex, a group of closely related and highly productive perennial C4 grass species in the subtribe Saccharinae that includes sugarcanes and miscanthus. Intergeneric hybrid “miscanes” have been made by crossing miscanthus with hybrid sugarcanes, suggesting that natural genetic variation in these two genera could be combined in order to blend desirable traits . Here we establish miscanthus as a genomic model for perenniality and polyploidy, and develop a foundation for genomic variation that will enable the future improvement of perennial biomass crops. We describe a draft chromosome-scale genome sequence for M. sinensis, prove that miscanthus is a paleoallotetraploid by analyzing the distribution of transposable elements across its genome, and establish the timing of key evolutionary events. By mRNA sequencing, we identify genes preferentially expressed in rhizomes, stems, and leaves, and explore the unique transcriptional dynamics of nutrient mobilization in this rhizomatous perennial grass. Unlike most perennial Andropogoneae, which are restricted to tropical or subtropical regions, the Miscanthus genus comprises species that naturally range from tropical to subarctic regions. Genomic analysis of 18 miscanthus accessions sequenced for this study, in addition to reduced representation genotyping of over 2000 accessions collected in the wild from east Asia, reveals extensive population structure and interspecific introgression, which further contributes to the genomic diversity of the genus Miscanthus.
We assembled the M. sinensis genome into n = 19 chromosomes by combining short read whole-genome shotgun and fosmid-end data with in vitro and in vivo chromatin proximity libraries . The reference accession is the previously characterized doubled haploid DH1, which as expected is homozygous throughout. The genome assembly anchors 1.68 Gb of contigs to chromosomes, with a contig N50 length of 33.1 kb and pre-HiC scaffolding N50 length of 190 kb . An additional 0.20 Gb of contig sequence in scaffolds is not yet placed on linkage groups; highly repetitive sequences are problematic and missing from the assembly . We validated the assembly at chromosome scale by comparison with an integrated genetic map with 4298 assignable markers . We predicted the structure of 67,967 protein-coding genes based on several lines of evidence, including homology with other grasses and deep transcriptome data for miscanthus and sugarcane. These predicted genes account for an estimated 98% of protein-coding genes, with 94% assigned to a chromosomal position . These genes are embedded within a sea of transposable element relicts and other repetitive sequences, which account for 72.4% of the M. sinensis genome assembly. The most common class of assembled transposons are gypsy long terminal-repeat retrotransposons . The paleotetraploidy of miscanthus is evident at the sequence level, since each sorghum chromosome aligns to a pair of M. sinensis chromosomes, after accounting for the chromosome fusion of ancestral sorghum 4- and 7-like chromosomes that reduces the karyotype from n = 20 to n = 19 . As expected from earlier genetic maps, the miscanthus and sorghum genomes show extensive 2:1 conserved collinear synteny , consistent with a whole-genome duplication in the Miscanthus lineage. While it has been suggested that this duplication could be shared with sugarcane, comparison of M. sinensis and S. spontaneum genomes shows that the duplications in the two lineages are distinct . Although the doubled genome and disomic genetics of miscanthus is suggestive of an allotetraploid history,flower pot wholesale neither a mechanism nor timing for paleotetraploidy has been described, in part due to the absence of known diploid progenitor lineages. We address this further below. Regarding the more than twofold difference in bulk genome size between sorghum and miscanthus, we find that lengths of coding sequence and introns are generally similar , with overall differences arising from increased intergenic spacing in miscanthus due to transposon insertion, as well as by the expansion of repetitive pericentromeric regions, which are only partially captured in the assembly . The chromatin conformation contact map exhibits an enrichment of centromeric and telomeric contacts, respectively, consistent with the interphase nuclear “Rabl” conformation as seen in the barley genome. We identified locally interacting chromosomal compartments for which A compartments have a higher gene density and B compartments have lower gene density and tend to occur predominantly in the pericentromeric region, as observed in other plants.An allotetraploid origin for a paleotetraploid species is commonly demonstrated by showing that one set of its chromosomes is more closely related to some diploid lineages to the exclusion of others. Because there are no known candidates for the diploid progenitors of tetraploid miscanthus, this approach cannot be used here. Instead, we used a new method that relies on the chromosomal distribution of repetitive elements, which can provide robust markers for sub-genome ancestry.
We sought repetitive sequences whose presence is enriched on one member of each homeologous chromosome pair . Such sequences are definitive markers of allotetraploidy, and occur as relicts of repetitive elements that were active in only one of the two diploid progenitors prior to hybridization and genome doubling. Importantly, the method does not require access to or even knowledge of living representatives of the progenitor lineages. We found 1187 13-bp sequences whose pairwise enrichment pattern consistently partitions homeologous chromosome pairs between distinct A and B sub-genomes . This observation establishes the past existence of distinct A and B progenitor lineages , and the allotetraploid origin of miscanthus. Although we can use these markers to assign each miscanthus chromosome in bulk to the A or B sub-genome, we find evidence for the balanced reciprocal exchange of distal segments between homeologous chromosomes such that dosage remains intact . Based on consistency with our dense genetic map, these are clearly bona fide homeologous exchanges rather than misassemblies. The observed distal reciprocal exchanges likely occurred either by mitotic recombination in the vegetative tissue of an AB F1 hybrid founder prior to genome doubling, or by aberrant homeologous recombination after allotetraploidy. The concentration of these exchanges toward the ends of chromosomes is consistent with the proximity of these regions in a telomeric bouquet conformation. The maintenance of discrete A/B patterns of diagnostic 13-mers in these distal segments implies that these exchanges occurred by single crossover events rather than recurring recombination throughout the distal regions of the chromosomes, which would blur the distinctive A/B 13-mer signature. Discrete homeologous exchanges are often observed in newly formed allotetraploids and are thought to occur in response to a new meiotic environment. In studies of other polyploids, homeologous replacements that alter the balance between A and B alleles are common; when such variants are segregating in apopulation, the resulting genetic variation can underlie quantitative trait loci. In contrast to these studies, however, in Miscanthus, we find predominantly balanced reciprocal exchanges that alter chromosomal linkage, but do not change A/B dosage, and no evidence that these segmental exchanges are segregating in our sequenced samples, suggesting that the reciprocal homeologous exchanges are the result of ancient events that have become fixed in Miscanthus. In addition to these long fixed reciprocal exchanges, there are several shorter internal homeologous segments that could correspond to nonreciprocal or recurrent exchange. These segments will be interesting to study further. From the identification of distinct A and B sub-genomes, we see that the sorghum-7 and -4-like chromosomes that fused to form miscanthus chromosome 7 were both derived from the B progenitor. While it is possible that the fusion occurred in the B progenitor itself prior to hybridization, the absence of other Saccharinae with n = 9 chromosomes, and the likelihood of chromosome instability in the aftermath of allotetraploidization, suggests that the fusion occurred after allohybridization. The timeline of paleotetraploidy in miscanthus can be established through inter- and intra-subgenome comparisons . We estimate that the A and B progenitors diverged from their common ancestor ~7.2 Mya , based on the synonymous differences between homeologous protein-coding genes . After this divergence but before hybridization, the two progenitors evolved independently; evidence of their species-specific transposable element activity appears in the contemporary Miscanthus genome as subgenome-specific repeats. Consistent with this hypothesis, we find several LTRretrotransposon families within only one of the two subgenomes, and estimate that they were actively inserting during the period ~2.5–6 Mya . In contrast, transposon activity after the allotetraploidy event should be distributed across the entire Miscanthus genome without regard to subgenomes. Also, consistent with this picture, we find a burst of transposon activity that is not subgenome-specific starting ~2.5 Mya, which serves as our best estimate for the allotetraploid origin of Miscanthus . Finally, the interfertile sister species M. sinensis and M. sacchariflorus diverged ~1.65 Mya , consistent with speciation occurring after allotetraploidy. Chromosome-level comparisons of repetitive elements and protein sequences confirm that the polyploidies of Miscanthus and sugarcane occurred independently . Common hallmarks of allopolyploidy are asymmetric gene loss and biased gene expression between subgenomes, which are both thought to arise from epigenetic asymmetries in the aftermath of allohybridization. Comparing miscanthus and sorghum genes, we find that ~29% of sorghum genes have been lost on one of two subgenomes; conversely, ~71% have co-orthologs on both subgenomes .