There were 50.1% of the reads that passed the filtering criteria and mapped uniquely to the G. max reference genome. These reads were used in the digital gene expression analysis of all 14 tissues. Of the 66,210 predicted gene models in G. max (consisting of 46,430 high-confidence models and 19,780 lower-confidence models), 49,151 (74.2%) genes were transcriptionally active by the following definition: having a sum of at least two counts in one or more tissues in this study (Additional file 2). In the Glyma1.01 annotation set , 46,430 genes were identified as \"high confidence\" as determined by the following criteria: correlation to full-length cDNAs, Expressed Sequence Tags, homology, and ab initio methods [12, Supplementary Information section 2]. Of those 46,430 highly-confident genes , 41,975 (90.4%) genes were transcriptionally active in this study (Additional file 3) and 4,455 (9.6%) highly-confident genes were not. Conversely, there are an additional 7,176 (10.8%) transcriptionally active gene models from the lower-confidence gene models (Additional file 4). These gene models will be evaluated for possible inclusion to the list of highly-confident gene models.
Given our limited understanding of the full complexity of the soybean genome, it is gratifying that only a small percentage (3.5%) of the reads that mapped uniquely were located outside the predicted gene models. This suggests that the initial annotation of the soybean genome sequence has captured the majority of transcriptional activity. Using the additional information on transcriptionally active regions, refinement of the existing gene models and the ability to identify new gene models will be improved.
The seeds were derived from introgressing G. soja (PI468916) into G. max (A81-356022). Specifically, the BC5F5 plant P-C609-45-2-2 was heterozygous for the LG I protein QTL introgression from G. soja. These seeds were planted directly into pots containing Bradyrhizobium japonicum-inoculated soil and supplemented with full nutrient fertilizer (Osmocote 14-14-14) in growth chambers at the University of Minnesota. Chambers were set initially to a photoperiod of 14/10 and thermocycle of 22C/10C and monitored to mimic Illinois field growing conditions. Relative humidity settings were 50-60%, and light intensity was measured at 550-740 μE m-2 sec-1. All harvests occurred at 1400 hours and consisted of samples pooled from a minimum of three plants . Samples were harvested from plants in parallel and flash frozen in liquid nitrogen before storage at -80C. Open flowers and young leaf tissue samples were collected simultaneously. Pods and seeds were harvested by seed weight and pod lengths that correspond to approximated Days After Flowering (DAF) as specified. The one-cm pod was processed intact (approximately 7-DAF), while the four and five cm pods (approximately 10-13 DAF and 14-17 DAF) were divided into seed and pod-shell components. Seed 21-DAF, Seed 25-DAF, Seed 28-DAF and Seed 35-DAF had seed weights between 10 and 25 milligrams, 25 and 50 milligrams, 50 and 100 milligrams, 100 and 200 milligrams, and greater than 200 milligrams, respectively.
Root and nodule tissues were harvested from plants grown in growth chambers set to 16-hr photoperiods with light intensities ranging from 310-380 μE m-2 sec-1. Seeds were imbibed for three days, planted in quartz sand and fertilized with a full nutrient solution. Root tissue was harvested after 12 days. Nodules were harvested at 20-25 days after inoculation; for these samples, plants were fertilized for the first seven days with nutrient solution containing 3.5 mM NO3 and subsequently fertilized every other day with a full nutrient solution lacking nitrogen.
The authors gratefully acknowledge financial support from the USDA-Agricultural Research Service, Current Research Information System (CRIS No. 3640-21000-024-00D) and CRIS No. 3625-21220-004-00D, and National Science Foundation Grant #0822258 We are also grateful for funding from the United Soybean Board. We thank Bruna Bucciarelli for assistance with tissue collection and sample preparation, Nathan Weeks for technical and IT support, Kevin Feeley for website implementation and Dan Nettleton for advice on statistical methods.
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Hi Travis, this was a very informative article, thank you. I am in grad school and besides my loan for grad school I also have a consolidated loan from my undergrad years that is on an in-school deferment. I currently have full time qualifying employment for PSLF but am still about 6 months away from graduating, so I have not yet made any qualifying payments and am not yet on a qualifying repayment plan for either of my loans.
Does that mean that once submitted, no future loans can be considered for forgiveness I have $80k in Direct loans now, but one more year of Graduate school loans to take out. I am a full-time community college professor.
I was told that they could discharge my obligations, but that it would just fall to my husband and daughter. I received letters in the mail stating which loans would go to my husband and which to my daughter. I believe three loans would be fully forgiven.
Hi!I have a question about managing my PSLF. I submitted my employer certification form last year and was certified for PSLF (I work full time for a community college) and entered into REPAYE. Does Fedloan add each month or do you have to recertify your employer every year to see the payments towards PSLF increase Also, as I understand it, in REPAYE the government pays all or some of the interest for direct loans while in the plan. But, my statements are showing that interest is continuing to accumulate although it has not yet been capitalized. What is going on here I tried to get information from Fedloan and they just directed me back to their website information on REPAYE. Very unhelpful! Any advice or insight you can give is much appreciated!
From PSLF Employment Certification Form: Full-time means working for one or more qualifying employers for the greater of: (1) An annual average of at least 30 hours per week or, for a contractual or employment period of at least 8 months, an average of 30 hours per week; or (2) Unless the qualifying employment is with two or more employers, the number of hours the employer considers full time.
Just curious if you knew if this meant that at minimum you have to work an average of 30 hours per week or that as long as the employer says that you are full-time that is what matters And does it just have to be for 8 months of the year (For example if you take a week or two off for vacation or something does that still count it)
I believe that the Fedloan Servicing is not correctly tallying/calculating the months I have made payments. I filed for PSLF forgiveness and also for the TPSLF. I have been making regular monthly payments for at least 8 years (maybe 10) and working full-time at the same qualifying 501 C-3 agency since 2006, but their system has my employer listed with three different names and many of the payments I made are not being counted. How do I independently check into this instead of taking their word for it
Finally, this situation does not affect public service loan forgiveness, as long as my employer considers me to be working full time during my leave time, correct I appreciate any advice you could provide.
Thank you for such an informative article! One question that I am still unsure of. I am starting grad school in the coming weeks and have a Direct Stafford Loan and I will be working full time at a qualifying non-profit while I am in school. Am I able to start working towards the 120 payments right away, or do I need to wait until I have graduated to begin the 10 year process Also, my direct loan does not cover the full cost of my annual tuition. If I supplement with a PLUS loan am I able to consolidate and still qualify Or will I need to pay the extra out of pocket and only put the direct loan towards PSLF Thank you! 59ce067264