1. PROCESS OF BRANCHING BUD INITIATION This bud will grow out (Bud outgrowth) - depending on developmental and environmental signals BRANCH WILL BE FORMED Lateral shoot branches are derived from axillary buds that arise in the leaf axils, that is -arising in the angle between a leaf and a stem. In some plants, buds may also form from the older parts of shoot or root remote from the main apices; these buds, termed adventitious, do not conform to the general plan.” http://www.britannica.com/EBchecked/topic/46162/axillary-bud A bud when formed at the leaf axil can outgrow to form a branch or can remain dormant and not form a branch A branch can be defined when a flower head is formed which can give rise to seeds (when vegetative tissue culminates into a reproductive structure)

2. Therefore we can score for 3 Important Phenotypes - with respect to main stem and central head BUD INITIATION NO BUD BRANCHES 1 2 3 Branch can be small or big in length, as long there is a flower head that might give rise to a seed it can be counted as a functional branch

3. A branch that comes from the leaf axil is the Primary (1 0 ) branch- This branch in turn may – again give rise to A) no branch; B) a bud or C) another branch (secondary -2 0 branch ) Primary (1 0 ) branch Secondary (2 0 ) branch 2 0 bud initiation 2 0 no bud A B C

4. The plant can be divided roughly into four quarters, since plants can be branched only at the top or bottom: The top and the bottom can be further divided into 2 quarters each dividing the plants into 4 quarters. Please use your discretion here:- If most of the branches are in the top half (and say for e.g. only one branch arises in the 3 rd or 4 th quarter) then divide the plant accordingly to indicate the branching is only in top half for all practical purposes, see diagram in the box. 1/4th 2/4th 3/4th 4/4th Top Half Bottom Half In this case just move the quarters slightly down

5. PLANT NAME Main stem with central headYES/NO TOPBOTTOM First 1/4thSecond 1/4thThird 1/4thFourth 1/4th BranchingYES/NO No of branches If nodes w/o br, initiation >50%YES/NO/NA Longest br length 2° br on longest 1° brYES/ NO If no 2° br is there initiationYES/NO 2° head dia in longest brBIGGER - SAME - SMALLER (in comparison to 1° head) Any extra Comments 1 2 3 4 5 6 7 9 8 For branching or no branching- make sure that it is not just one odd node in the whole plant showing branching or not branching- it might be something unusual. You can note that down in your comments. For e.g. Only one node seen with initiation in the 3 rd quarter. It will become more clear in the following slides. PHENOTYPES TO BE SCORED

6. 1 PLANT NAME Main stem with central headYES/NO 1 PLANT NAME Main stem with central headYES/NO For this particular e.g. phenotyping should be similar: Just mention how many heads and if the head size is similar. Also choose one as the main stem and phenotype it, for the remaining stems just make comments if different from the one you have phenotyped.

7. TOPBOTTOM First 1/4thSecond 1/4thThird 1/4thFourth 1/4th BranchingYES/NO No of branches If nodes w/o br, initiation >50%YES/NO/NA 2- If plant does not branch Pointers: Sometimes the leaf might be absent especially at the bottom since they may have just dried out. Also the bud might be v. v. small and not very discernable but take a closer look, generally the pattern would be similar, if you see buds in the lower half it might be till the very bottom-most axil although it might be brownish and dry. This plant has no branching:- NO branching in all quarters No of branches: Does not apply if no branching so leave it blank If nodes w/o br, initiation >50%: This point might be confusing, but will be explained many times with diff examples. For e.g. in this case in the 1 st 1/4 th there are 2 nodes that show bud initiation of three (which is equal to or greater than 50% and therefore YES. The remaining quarters will be no, although the 2 nd 1/4 th has one bud, but it is one bud of four which is only 25% (so NO). NA (Not Applicable): This option is only for plants that branch – Next Slide. 1 st 1/4th 2 nd 1/4th 3 rd 1/4th 4 th 1/4th Top Half Bottom Half 2 4 3

8. TOPBOTTOM First 1/4thSecond 1/4thThird 1/4thFourth 1/4th BranchingYES/NO No of branches 3 2 If nodes w/o br, initiation >50%YES/NO/NA 2- If plant branches  There could be 6 possibilities - For branching (#2) and If nodes w/o br, initiation >50% (#4) - (YES/YES, YES/NO, YES/NA, NO/YES, NO/NO, NO/NA).  Explained in next slide with e.g  Also for If nodes w/o br, initiation >50%, it means that count the leaf axils that have no branching in a particular quarter and then see if among them 50% or more show initiation  Also for phenotyping it might be best to finish, 2, 3, and 4 for First 1/4 th, then go to the Second 1/4 th and so on. It will be faster.  It will also help if the 1st person reads out and a 2 nd person repeats the reading back to the 1 st person who notes down the reading.  If you are confused about some parameter in a plant, It would be best to see the pattern among the remaining 3 replicates and that would give you a feel too.  Also, if you see something odd like only one node that has initiated when all the remaining nodes have branched, use your discretion to make the reading (you can make a comment that you saw only one node that has initiation/branching). 2 4 3

9. TOPBOTTOM First 1/4thSecond 1/4thThird 1/4thFourth 1/4th BranchingYES/NO No of branches 3 2 If nodes w/o br, initiation >50%YES/NO/NA 2- If plant branches Branching: No No of branches: Keep it blank If nodes w/o br, initiation >50%: Yes, 2 of 3 nodes have initiated Branching: Yes No of branches: 4 If nodes w/o br, initiation >50%: NA, it suggest that all the nodes in that quarter shows branching. This parameter will tell you if all the nodes have branches. The answer would have been NO only if a leaf axils did not branch and did not show initiation (like in 3/4 th and 4/4 th ). Branching: Yes No of branches: 2 If nodes w/o br, initiation >50%: No since 50% of the nodes show no branching and no initiation Branching: No, In this case there is no branch. No of branches: Keep it blank If nodes w/o br, initiation >50%: No since all of the nodes show no branching and no initiation  Other cases: IF branching is NO, then for nodes with If nodes w/o br, initiation >50% Yes or no is the only possibility (NA is not a possibility)  The last case could be: If branching is YES and there were many nodes with branches and nodes with initiation only, then for nodes with If nodes w/o br, initiation >50% you need to answer YES. 1/4th 2/4th 3/4th 4/4th Top Half Bottom Half 2 4 3

10. TOPBOTTOM First 1/4th Second 1/4thThird 1/4thFourth 1/4th BranchingYES/NO No of branches 3 4 (labeled) If nodes w/o br, initiation >50%YES/NO/NA If plant has absolute basal branches- Make a note 2 4 3 NOTE: Of which 3 were Absolute Basal branches. Length: X cms, had no 2 0 branches but had initiation (see branch 2 and 3). 2 of the absolute basal branches had similar length and head diameter was smaller. 1/4th 2/4th 3/4th 4/4th Top Half Bottom Half 1 3 4 X cms 2 With the remaining phenotyping we proceed as in the next few slides. The longest branch length will be in the second 1/4 th and we measure it-See next slide. We do not include the absolute basal branches for the rest of the phenotyping (This point can be discussed if not clear). ONE more POINT: We saw that basal branching was influenced planting density and only if possible we mad a note of that

11. First 1/4thSecond 1/4thThird 1/4thFourth 1/4th Longest br length 13 inches  Go through the plant and select the longest branch  Measure it with a ruler  Write it down:- in whichever quarter it is in  For e. g. A: it is in the Third 1/4 th  Now just quickly go through the remaining plant and see it any more branches have similar length, just eye-ball it.  In Plant A no other branches have as long a branch and so keep all the remaining blank (so we know that it was smaller in all the remaining quarter)  In e.g. B you would have put the longest branch reading in Third 1/4 th.  But now when you scan through the plants you can see that there is one similar sized branch in Fourth 1/4 t. Just write “E” (for equal) in Fourth 1/4 th  You don’t have to measure it, just eye-ball it, if it looks almost similar then write E  Leave the remaining blank  THIS WILL TELL US SOMETHING ABOUT THE PLANT ARCHITECTURE. Some plants may have equal sized branches in all the four quarters e.g. A e.g. B First 1/4thSecond 1/4thThird 1/4thFourth 1/4th Longest br length 13 inches E eg A eg B 5 5

12. 2° br on longest 1° brYES/ NO If no 2° br is there initiationYES/NO 2° head dia in longest brBIGGER - SAME - SMALLER (in comparison to 1° head) 6 7 8  6, 7, and 8 - All these readings are in the longest branch  So once you measure the longest branch length look for all the remaining phenotypes  For 6: Slide 3 explains secondary branches (2°)  Just circle YES of NO  For 7: If there is no branch then see if there is initiation, again YES or No  For 8: Just look at the head in the secondary branch (2°), this will be the 2° head and see if it is bigger, same or smaller than 1° head (central head) – no need to measure, just make a good accurate guess.

13. Any extra Comments 9 Any comments such as  Tertiary 3 0 branches  If the plant has only one branch, like an odd branch  Or anything you see interesting or peculiar