2. Materials and Methods
3.5 Coincidence of genome-wide associations across traits
Results
74
Results
75
structuring of the traits. PCA with iSelect results explained same proportion of variation, only the resolution of the separation of traits from each other changed (Fig 3.41, 3.42, 3.43).
Similarly PCA was performed with GWAS results using BOPA1 SNPs in HVCC_S gene pool.
PC1 explained 15.11 percent of variation (Sup. Fig S10). Traits like rowed type, GEar, Gwidth and TGW clustered separately from the all other traits (Sup. Fig S8, S9). PC2 explaining 12.5 percent of variation, separates traits like Glength, W_L, Gwidth, TGW, GEar and row type.
Traits like yield, starch content, spike length, heading, height, protein and PM field and PM detached leaf assay were clustered together (Sup. Fig S8, S9). Similar structuring of the traits was observed with PCA constructed using results of GWAS with iSelect SNPs (Sup Fig S10).
Only exception observed was for the traits spike length and plant height. (Sup. Fig S8, S9).
Results
76 (a)
(b)
Fig 3.41: Principal component analysis of the associations in winter barley. Significant principal components (PC1 and PC2) are shown using (a) BOPA1 and (b) iSelect SNP markers
Results
77 1H 2H
GWA for multiple traits in winter barley gene pool
11_10654 11_11223 11_21354 11_21067 11_10419 11_21226 11_10332 11_10775 11_10030 11_20371 11_20712 11_10873 11_10186 11_10757 11_10744 11_20617 11_10760 11_10814 11_10764 11_20514 11_10275 11_10597 11_21134 11_10259 11_10526 11_10294 11_11064 11_10470 11_11478 11_10438 11_20660 11_20427 11_21193 11_20698 11_11484 11_21357 11_21312 11_20810 11_20912 11_21000 11_10833 11_11359 11_21217 11_10933 11_21361 11_10075 11_10520 11_10293 11_10324 11_21053 11_21333 11_10768 11_10552 11_20997 11_11049 11_10798 11_10617 11_20432 11_21431 11_10516 11_10043 11_11367 11_20956 11_10002 11_20290 11_10686 11_11075 11_21126 11_10006 11_20121 11_20990 11_20434 11_20550 11_20792 11_11189 11_21446 11_20475 11_21373 11_10396 11_11277 11_10522 11_20754 11_20169 11_10357 11_20909 11_20267 11_20921 11_20625 11_20844 11_10789 11_21392 11_10729 11_20959 11_10854 11_10911 11_21038 11_20908 11_10586 11_10722 11_21140 11_11481 11_10644 11_20383 11_10782 11_20603 11_21384 11_11105 11_20138 11_10590 11_20915 11_20772 11_10443
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RowRowRowRow Hd SlSlSl GEarGEarGEarGEar YldYldYld TGW TGW GareaGareaGarea GWidthGWidthGWidth GlengthGlength W_lW_lW_l FrFrFr PCPCPCPC PMdlaPMdla
1H
11_10326 11_11059 11_21377 11_20563 11_20724 11_10180 11_10216 11_21015 11_20394 11_21366 11_21265 11_21261 11_10787 11_10891 11_20864 11_21304 11_10525 11_10178 11_10399 11_10919 11_10837 11_21153 11_10648 11_21338 11_10498 11_11505 11_21005 11_11054 11_20674 11_10297 11_11302 11_10422 11_10638 11_20929 11_11522 11_11400 11_10147 11_10325 11_20387 11_10733 11_11015 11_20748 11_10997 11_10602 11_10796 11_11133 11_11354 11_11046 11_10012 11_10679 11_20476 11_10070 11_20039 11_10624 11_20251 11_11384 11_10436 11_10632 11_20585 11_20390 11_10191 11_10685 11_10692 11_21399 11_11430 11_20374 11_21166 11_21144 11_10265 11_21251 11_21205 11_20667 11_20528 11_20947 11_20419 11_10818 11_11435 11_20699 11_10196 11_10823 11_10619 11_10786 11_21242 11_11214 11_20781 11_11100 11_10287 11_10213 11_11533 11_10475 11_21037 11_11058 11_21351 11_10214 11_20080 11_21007 11_10138 11_21175 11_11307 11_10876 11_11250 11_10398 11_10900 11_10731 11_21238 11_11043 11_10990 11_10429 11_11236 11_20182 11_10538 11_10916 11_10780 11_21220 11_20511 11_11365 11_21315 11_21370 11_21440 11_20480 11_21459 11_11486 11_10109 11_21088 11_20366 11_10656 11_10065 11_20215 11_11227 11_20590 11_10826 11_10566 11_10315 11_11380 11_21346 11_20293 11_20943 11_21099 11_21453 11_10085
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RowRowRowRow HdHdHd HtHtHt SlSl GEarGEarGEar GEar TGW GareaGarea GWidth GWidth GWidthGWidth GlengthGlength W_lW_lW_lW_l FrFr PCPCPC PC SCSC PMdla PMfldPMfld
2H
Results
78
3H 4H
4H
11_20252 11_21398 11_21027 11_10886 11_10112 11_20595 11_20172 11_10565 11_10559 11_20794 11_20607 11_10026 11_10672 11_10710 11_20410 11_10825 11_10081 11_10863 11_21145 11_20647 11_10601 11_21101 11_11313 11_21197 11_10380 11_11086 11_10328 11_20970 11_11502 11_11501 11_10137 11_20796 11_10456 11_20583 11_10620 11_11283 11_20801 11_20856 11_21062 11_21147 11_10925 11_10926 11_10966 11_21435 11_21472 11_11124 11_20486 11_20439 11_20428 11_11530 11_11337 11_20002 11_10008 11_10011 11_20102 11_11125 11_10349 11_20333 11_10224 11_20288 11_20444 11_11401 11_10225 11_20276 11_11016 11_10373 11_10158 11_10653 11_10728 11_10281 11_21120 11_11191 11_11391 11_10839 11_10335 11_20704 11_21305 11_20931 11_10172 11_20017 11_11394 11_11314 11_11241 11_20694 11_10350 11_10276 11_20566 11_20695 11_10683 11_20778 11_10047 11_20597 11_20362 11_21358 11_20093 11_20063 11_10444 11_10628 11_20659 11_10747 11_11021 11_21438 11_20628 11_20999 11_10515 11_10184 11_21083 11_21381 11_21495 11_21493 11_20009 11_21513 11_20023 11_21161 11_21212 11_20523 11_10753 11_21277 11_11503 11_10312 11_11330 11_20944 11_21405 11_10918 11_11172 11_10754 11_10821 11_10867 11_20343 11_10280 11_11141 11_11196 11_20612 11_10842 11_20527 11_21428 11_10381 11_11127 11_11328 11_20920 11_21427 11_20851 11_10631 11_21266 11_21272 11_11436 11_21008 11_10646 11_10702 11_20605 11_10681 11_11410 11_21267 11_10694 11_11516 11_10767 11_10283 11_10343 11_21362
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Row HdHtHt SlSl YldYldYldYld TGW GareaGareaGarea GWidthGWidth GlengthW_l FrFrFr PCPCPCPC PMdlaPMdla PMfld
3H
11_20145 11_10208 11_10409 11_21056 11_21228 11_11345 11_10319 11_10113 11_10738 11_10223 11_20557 11_10574 11_21359 11_10221 11_21385 11_20210 11_10132 11_20109 11_21418 11_21070 11_20680 11_20606 11_20302 11_20777 11_20001 11_21374 11_21122 11_20411 11_20012 11_20180 11_20114 11_11180 11_10048 11_10668 11_10793 11_20939 11_21490 11_11405 11_20853 11_21073 11_10756 11_21071 11_10577 11_20269 11_10093 11_20782 11_10942 11_20496 11_11042 11_11332 11_10946 11_11114 11_20610 11_10881 11_11244 11_10046 11_10527 11_20412 11_10262 11_20020 11_10568 11_21481 11_20361 11_21191 11_21087 11_11207 11_21296 11_20453 11_20820 11_20723 11_11224 11_20924 11_20906 11_10639 11_10052 11_20062 11_11229 11_10010 11_10606 11_20072 11_20580 11_11513 11_21504 11_10467 11_10829 11_20815 11_10309 11_10090 11_10523 11_11500 11_20670 11_20197 11_10724 11_20689 11_10723 11_11213 11_20765 11_11398 11_10588 11_20732 11_21243 11_20119 11_10614 11_11470 11_20515 11_20454 11_10510 11_10334 11_21111 11_20974 11_11299 11_11066 11_21035 11_10611 11_21210 11_10610 11_20007 11_10387 11_20013
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Row RowRowRow Row HtHt SlSlSl Yld GEarGEar GEarGEarGEar GEarGEar TGWTGWTGW GareaGareaGarea GWidthGWidthGWidth GlengthGlength W_lW_lW_lW_l FrFrFr PCPCPC PC SCSCSC PMdla
4H
Results
79
5H 6H
11_20553 11_20206 11_11381 11_21221 11_20010 11_20873 11_10974 11_21426 11_11048 11_10688 11_10580 11_10621 11_20980 11_21391 11_20845 11_20729 11_10260 11_20571 11_10955 11_20987 11_11432 11_21401 11_11198 11_21447 11_20841 11_21308 11_10116 11_20129 11_20700 11_10995 11_21350 11_21011 11_20958 11_10058 11_21215 11_21260 11_20461 11_10661 11_11128 11_20737 11_11260 11_21318 11_21536 11_20306 11_10671 11_10840 11_20372 11_11240 11_20961 11_11159 11_20265 11_11281 11_20441 11_21344 11_20713 11_21275 11_21121 11_21239 11_11249 11_20392 11_21001 11_20367 11_20236 11_10167 11_20736 11_11355 11_20645 11_21445 11_21480 11_11290 11_10578 11_20097 11_11473 11_10771 11_10518 11_20449 11_20850 11_10622 11_21421 11_20327 11_10414 11_20549 11_21314 11_20795 11_21168 11_11273 11_10477 11_11341 11_11200 11_10094 11_20629 11_20127 11_11456 11_10360 11_20653 11_20347 11_20003 11_11024 11_20300 11_10805 11_20259 11_10705 11_11090 11_21247 11_21177 11_10095 11_21241 11_11080 11_11071 11_11532 11_10755 11_10845 11_21289 11_20375 11_10292 11_11092 11_21077 11_20676 11_20731 11_10557 11_20791 11_21297 11_10080 11_10363 11_11441 11_21355 11_11490 11_11497 11_10901 11_11185 11_10820 11_21041 11_10741 11_20545 11_10582 11_21452 11_10902 11_21024 11_20078 11_21018 11_10336 11_20988 11_11216 11_20546 11_10869 11_10778 11_10254 11_21138 11_20189 11_20897 11_10310 11_21052 11_11364 11_10401
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HdHd HtHtHtHtHtHt SlSlSlSlSl YldGEar TGWTGW GareaGareaGarea GWidth GWidthGWidth GlengthGlengthGlength W_lW_l FrFrFrFr PCPC SCSCPMfld PMfld PMdla PMdla
5H
11_20493 11_20881 11_20886 11_10669 11_21521 11_20882 11_21204 11_21032 11_11479 11_20415 11_10165 11_10023 11_21246 11_10136 11_20315 11_10868 11_10676 11_10939 11_10427 11_20052 11_10129 11_10882 11_10061 11_10244 11_20936 11_21281 11_10462 11_20743 11_10013 11_11097 11_20707 11_10817 11_10539 11_10461 11_20291 11_20675 11_11205 11_20720 11_10003 11_21473 11_21158 11_20651 11_10962 11_21014 11_20600 11_11312 11_21216 11_21124 11_10848 11_20946 11_10323 11_11153 11_20572 11_20799 11_20854 11_10513 11_20835 11_10227 11_20184 11_11067 11_21339 11_10964 11_20266 11_20058 11_10270 11_10635 11_21310 11_21298 11_11483 11_21069 11_20904 11_20287 11_10455 11_21225 11_11261 11_20709 11_10124 11_10040 11_20015 11_20714 11_20468 11_20636 11_21469 11_20620 11_20892 11_20577 11_11349 11_20784 11_11459 11_21256 11_20488 11_20053 11_20889 11_20969 11_21224 11_10608 11_11458 11_10220 11_10331 11_10185 11_11246 11_21404 11_11147 11_20654 11_10815 11_10400 11_20783 11_21025 11_10202 11_20996 11_20728 11_11294 11_10595 11_20972 11_10978 11_10734 11_20531 11_10139 11_20118 11_10015 11_20379 11_20467 11_20036 11_20725 11_20355 11_20733 11_10239 11_11534 11_10107 11_10175 11_21455 11_11187 11_20005 11_11488 11_10748 11_20868 11_20687 11_21112 11_11111 11_20537
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RowRow HdHtHt SlSlSlSl Yld GEar TGWTGW Garea GWidth GlengthGlengthGlength W_lW_l FrFrFrFr PCPC PMfldPMfld PMdlaPMdlaPMdla
6H
Results
80 7H
11_21443 11_10121 11_11179 11_20307 11_20245 11_10841 11_10851 11_20755 11_21050 11_10025 11_20495 11_10965 11_20162 11_10920 11_20758 11_10451 11_10232 11_20192 11_20993 11_10838 11_10056 11_10327 11_21326 11_20249 11_10772 11_20790 11_20113 11_10726 11_11014 11_10346 11_10721 11_20975 11_10050 11_11098 11_21270 11_20750 11_20671 11_10431 11_20195 11_11122 11_10153 11_10299 11_10924 11_20879 11_10394 11_20911 11_10073 11_20460 11_20200 11_10055 11_10773 11_11145 11_21302 11_21335 11_11219 11_11352 11_10370 11_10534 11_20205 11_10069 11_10442 11_10531 11_11445 11_20896 11_20230 11_20042 11_20771 11_21409 11_10303 11_20083 11_20103 11_10169 11_20385 11_20092 11_10853 11_20652 11_20570 11_20247 11_11243 11_10182 11_21229 11_10861 11_10078 11_10797 11_10454 11_20847 11_10687 11_20139 11_10550 11_21363 11_20452 11_11440 11_10130 11_11275 11_20962 11_20117 11_20504 11_21086 11_10999 11_20170 11_20365 11_10174
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RowRowHd HtHt SlGEar TGWTGW GareaGareaGarea GWidthGWidth GlengthFr SCSC PMfldPMfld PMdla
7H
Fig 3.42: Genome-wide association of all traits in winter (HVCC_W) barley gene pool using BOPA1 SNP markers. Chromosome 1H-7H are shown along with the associated chromosomal regions highlighted as bars of various color according to the traits. Short abbreviations for traits are shown viz. Frost (Fr), row type (Row), height (Ht), heading (Hd), spike length (Sl), grains per ear (GEar), thousand grain-weight (TGW), grain area (Garea), grain length (Glength), grain width (Gwidth), grain width / length (W_l), starch content (SC), protein content (PC), powdery mildew resistance in field (PMfld) and powdery mildew detached leaf assay resistance (PMdla). Significant associated regions are shown (-log10
P ≥ 2) as bars of different colors
Results
81
1H 2H
GWA for multiple traits in winter barley gene pool
11_10654 11_11223 11_21354 11_20502 11_21067 11_10419 11_21226 11_10332 11_10775 11_10030 11_20371 11_20712 11_10873 11_10186 11_10757 11_10744 11_21048 11_20617 11_10814 11_10764 11_20514 11_10275 11_10597 11_21134 11_10259 11_10526 11_10438 11_11484 11_21357 11_21312 11_20810 11_21000 11_10833 11_11359 11_21217 11_10933 11_21361 11_10075 11_10520 11_10293 11_10324 11_21053 11_21333 11_10768 11_10552 11_20997 11_20432 11_21431 11_10516 11_10043 11_11367 11_20956 11_10002 11_20290 11_20229 11_10686 11_21126 11_10006 11_20121 11_20990 11_10279 11_10466 11_11037 11_10434 11_20434 11_20550 11_21192 11_10471 11_11189 11_21446 11_21373 11_20769 11_10396 11_11277 11_10522 11_20754 11_20169 11_10357 11_20909 11_20267 11_20780 11_20921 11_20625 11_20844 11_20021 11_10789 11_21392 11_10729 11_20959 11_10854 11_10911 11_21038 11_20908 11_10586 11_10722 11_21140 11_11481 11_11038 11_20383 11_10782 11_20603 11_21384 11_11105 11_11509 11_20594 11_20840 11_20138 11_10590 11_20915 11_20772 11_10443
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RowRow RowRowRow RowRow HtHtHt SlSl GEarGEar GEarGEarGEarGEar YldYld TGW TGWTGWTGWTGW TGW GareaGareaGarea GWidthGWidth GWidth Glength Glength GlengthGlength W_lW_lW_lW_lW_l PCPCPCPC SCSCSCSC PMdla PMdlaPMdla
1H
11_10326 11_11059 11_21377 11_20563 11_10943 11_10180 11_10216 11_21015 11_20394 11_21366 11_21265 11_21261 11_21187 11_10787 11_10891 11_20864 11_21304 11_10525 11_10178 11_10399 11_10919 11_10837 11_21153 11_10648 11_21338 11_10084 11_10498 11_21005 11_11054 11_20674 11_10297 11_11302 11_10422 11_10638 11_20929 11_11522 11_21096 11_21388 11_10325 11_20387 11_10733 11_11015 11_20748 11_10997 11_10796 11_10679 11_20476 11_20251 11_11384 11_10191 11_10685 11_10692 11_10909 11_21166 11_10265 11_21251 11_21205 11_20667 11_10818 11_11435 11_20699 11_10196 11_10823 11_10619 11_10786 11_21242 11_11214 11_20781 11_11100 11_10287 11_10213 11_11533 11_10475 11_21037 11_21136 11_21351 11_10214 11_20080 11_21007 11_10138 11_21175 11_11307 11_20923 11_10876 11_11250 11_10398 11_10900 11_21340 11_10630 11_11323 11_11094 11_20064 11_10988 11_10731 11_21238 11_11118 11_11043 11_10990 11_10989 11_10429 11_11236 11_20182 11_10538 11_10707 11_10404 11_10916 11_10780 11_20511 11_11365 11_21315 11_10446 11_21370 11_21440 11_20480 11_21406 11_21459 11_11486 11_10109 11_21088 11_20366 11_10656 11_21125 11_10065 11_20215 11_10383 11_10376 11_20895 11_20715 11_20590 11_21274 11_10625 11_20494 11_10551 11_10826 11_11262 11_10566 11_10315 11_21250 11_11380 11_21346 11_20994 11_20293 11_20943 11_21099 11_21453 11_10085 11_20561 11_20681
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RowRowRowRowRow HdHdHd HtHtHtHt SlSlSlSl GEarGEarGEarGEarGEarGEar YldYldYldYldYld TGWTGWTGW TGWTGWTGWTGW GareaGareaGareaGareaGareaGareaGareaGarea GWidthGWidth GWidthGWidth GlengthGlength GlengthGlengthGlengthGlength Glength W_lW_lW_l PCPCPC SCSC PMdlaPMdla PMfldPMfld
2H
Results
82
3H 4H
11_20159 11_11453 11_20252 11_21398 11_21027 11_20976 11_10886 11_10112 11_20595 11_20172 11_20742 11_10565 11_20552 11_10559 11_20794 11_20607 11_10672 11_10710 11_20410 11_10825 11_10081 11_10863 11_21145 11_20647 11_10601 11_21101 11_11313 11_21197 11_21109 11_10380 11_11258 11_21129 11_11086 11_10328 11_20970 11_11502 11_11501 11_10137 11_20796 11_10456 11_20583 11_10620 11_11283 11_20801 11_20856 11_21062 11_21147 11_10925 11_10926 11_10966 11_21435 11_21472 11_11124 11_20486 11_20439 11_20428 11_11530 11_11337 11_20002 11_10008 11_10011 11_20102 11_11125 11_10349 11_20333 11_10224 11_20288 11_11401 11_10225 11_20276 11_20995 11_11016 11_10373 11_10158 11_10653 11_10728 11_10281 11_21120 11_11191 11_11391 11_10839 11_10335 11_20704 11_21305 11_20931 11_10172 11_20017 11_11394 11_11314 11_20273 11_11241 11_20694 11_10350 11_20521 11_10276 11_20566 11_20695 11_10683 11_20778 11_10047 11_20597 11_20362 11_20115 11_21358 11_20093 11_20063 11_10444 11_10628 11_21294 11_20136 11_20659 11_10747 11_11021 11_21438 11_20628 11_20999 11_10515 11_10184 11_21083 11_21381 11_21495 11_20009 11_21513 11_20023 11_21161 11_21212 11_20523 11_10753 11_20168 11_21277 11_11503 11_10312 11_20944 11_21405 11_10918 11_11172 11_10754 11_10821 11_10867 11_20650 11_20343 11_10280 11_11141 11_11196 11_20612 11_20527 11_21428 11_10381 11_11127 11_20085 11_11328 11_20920 11_21427 11_20851 11_10631 11_21266 11_21272 11_20155 11_11436 11_21008 11_10646 11_10702 11_20605 11_10681 11_11410 11_21267 11_10694 11_11516 11_10283 11_10343 11_21362
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RowRowRowRowRowRow HdHd HtHt SlSlSl Yld YldYld TGW GareaGareaGarea GWidthGWidthGWidthGWidth Glength W_l W_lW_l PCPCPCPCPC SCSCSC PMdla PMdla PMfldPMfldPMfldPMfldPMfld
3H
11_20145 11_10208 11_10409 11_21056 11_21228 11_11345 11_10319 11_10113 11_10738 11_10223 11_20557 11_10574 11_21359 11_10221 11_21385 11_11136 11_20210 11_10132 11_20109 11_21418 11_21070 11_20680 11_20606 11_20302 11_20777 11_20001 11_10031 11_21374 11_21122 11_20411 11_20012 11_20114 11_11180 11_10048 11_10668 11_10793 11_20939 11_21490 11_11405 11_21073 11_10756 11_21071 11_10577 11_10261 11_20269 11_10093 11_20782 11_10942 11_10411 11_20496 11_10480 11_11042 11_11332 11_10946 11_11114 11_20610 11_10881 11_11244 11_10046 11_10527 11_20412 11_10262 11_20020 11_10568 11_21481 11_20361 11_21191 11_21087 11_11207 11_21296 11_20453 11_20820 11_20723 11_11224 11_20924 11_20906 11_10639 11_10052 11_20062 11_11229 11_10010 11_10606 11_20072 11_20451 11_20580 11_11513 11_21504 11_10467 11_10829 11_11319 11_10309 11_10523 11_11500 11_20670 11_20197 11_10724 11_20689 11_10723 11_20178 11_20765 11_11398 11_20358 11_10588 11_20732 11_10785 11_11292 11_21243 11_20762 11_20119 11_10614 11_11470 11_20515 11_20454 11_10510 11_10334 11_21111 11_20974 11_10123 11_10712 11_11299 11_20701 11_11066 11_21035 11_10611 11_21210 11_10610 11_20272 11_20007 11_10387 11_11186 11_20013 11_11019
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RowRowRowRowRowRow HdHdHd HtHtHt SlSlSlSl YldYld GEarGEarGEarGEar TGWTGWTGWTGWTGW TGW GareaGareaGareaGareaGarea GWidthGWidthGWidth GlengthGlength Glength GlengthGlength W_lW_lW_lW_lW_l PCPCPCPC SCSCSCSC PMdlaPMdla PMfldPMfld
4H
Results
83 5H 6H
11_20226 11_20894 11_20553 11_20206 11_11381 11_21221 11_20010 11_10695 11_20873 11_10974 11_21426 11_11048 11_21324 11_10688 11_10580 11_10621 11_20980 11_21391 11_20845 11_20729 11_10260 11_20571 11_10955 11_20987 11_11432 11_21401 11_11198 11_21447 11_20841 11_21308 11_10116 11_20129 11_20700 11_10995 11_21350 11_21011 11_20958 11_10058 11_21215 11_21260 11_20332 11_20461 11_10661 11_11128 11_11506 11_20737 11_11260 11_21318 11_21536 11_20105 11_21148 11_20306 11_20501 11_10671 11_10840 11_20372 11_11240 11_20961 11_11159 11_11221 11_21200 11_20265 11_11281 11_20441 11_21344 11_20713 11_21275 11_21121 11_21239 11_10641 11_11249 11_20392 11_21001 11_20367 11_20236 11_11355 11_20645 11_21480 11_11290 11_10578 11_20526 11_11473 11_10771 11_10518 11_20449 11_20850 11_10622 11_21421 11_20327 11_10414 11_11350 11_20018 11_10024 11_20549 11_10834 11_21314 11_20320 11_20795 11_21168 11_21061 11_11273 11_10477 11_11341 11_11200 11_10094 11_20629 11_20637 11_20127 11_11507 11_11456 11_10360 11_21325 11_20653 11_20347 11_20003 11_20300 11_10805 11_20259 11_20298 11_10705 11_11090 11_21247 11_21177 11_10783 11_10095 11_20884 11_21241 11_11080 11_11071 11_11532 11_10755 11_10845 11_21289 11_20375 11_10292 11_11092 11_21077 11_20676 11_20568 11_20731 11_20791 11_21297 11_10363 11_11441 11_10217 11_20104 11_10589 11_21355 11_11490 11_11497 11_10901 11_11185 11_10820 11_21041 11_10741 11_20545 11_10536 11_10582 11_21452 11_10902 11_21024 11_20078 11_20876 11_20560 11_21018 11_10336 11_20988 11_20646 11_11464 11_20829 11_11216 11_20546 11_20686 11_10869 11_10778 11_20536 11_10254 11_21138 11_20189 11_20897 11_21155 11_10310 11_21052 11_10401 11_20402 11_20132
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RowRow RowRowRowRow Row HdHdHdHdHdHd HtSlSl YldYldYld GEarGEarGEarGEarGEar TGWTGWTGW TGW GareaGareaGarea GWidthGWidthGWidth GWidth GlengthGlengthGlengthGlength W_lW_lW_l PCPCPC PMfldPMfldPMdla
5H
11_20493 11_20881 11_20886 11_10669 11_21521 11_20882 11_20294 11_21204 11_20262 11_21032 11_11479 11_20415 11_10165 11_10023 11_21246 11_10136 11_20315 11_10868 11_10676 11_10799 11_10939 11_10427 11_20052 11_10129 11_10882 11_10061 11_10244 11_20936 11_21281 11_10462 11_20743 11_10013 11_11097 11_20707 11_10817 11_10539 11_10461 11_20291 11_11205 11_20720 11_10003 11_21473 11_21158 11_20651 11_10962 11_21014 11_20600 11_11312 11_21216 11_21124 11_10848 11_20946 11_10323 11_20572 11_20799 11_20854 11_10513 11_20835 11_10227 11_20184 11_11067 11_21339 11_10964 11_20266 11_20058 11_10270 11_10635 11_21310 11_21298 11_11483 11_21069 11_20904 11_20287 11_10455 11_21225 11_11261 11_20709 11_10124 11_10040 11_20714 11_20468 11_20636 11_20620 11_20892 11_20577 11_11349 11_20784 11_11459 11_21256 11_20488 11_20053 11_20889 11_21224 11_10608 11_11458 11_10220 11_10331 11_10185 11_11246 11_21404 11_11147 11_10815 11_10400 11_20783 11_21025 11_10202 11_20996 11_20728 11_11294 11_10595 11_20972 11_10978 11_10734 11_20531 11_10139 11_20118 11_10015 11_20379 11_20467 11_20036 11_20725 11_20355 11_20733 11_10239 11_11534 11_10107 11_10175 11_21455 11_11187 11_20005 11_10748 11_20868 11_20687 11_21112 11_11111 11_20537
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RowRowRow HtHtHt YldYldYldYld GEarGEar TGWTGW TGWTGWTGWTGW GareaGareaGarea GareaGareaGarea GWidthGWidthGWidth GlengthGlength GlengthGlength Glength GlengthGlength W_lW_lW_l PCPC SC SC PMfld
6H
Results
84 7H
Fig 3.43: Genome-wide association of all traits in spring (HVCC_S) barley gene pool using BOPA1 SNP markers.
Chromosome 1H-7H are shown along with the associated chromosomal regions highlighted as bars of various color according to the traits. Short abbreviations for traits are shown viz. row type (Row), height (Ht), heading (Hd), spike length (Sl), grains per ear (GEar), thousand grain-weight (TGW), grain area (Garea), grain length (Glength), grain width (Gwidth), grain width / length (W_l), starch content (SC), protein content (PC), powdery mildew resistance in field (PMfld) and powdery mildew detached leaf assay resistance (PMdla).
Significant associated regions are shown (-log10 P ≥ 2) as bars
11_21443 11_21307 11_10121 11_20710 11_20242 11_11495 11_20534 11_20307 11_20245 11_10841 11_10851 11_20755 11_21437 11_21050 11_10025 11_20495 11_10965 11_20162 11_10920 11_20758 11_10451 11_10232 11_20192 11_20993 11_20126 11_10838 11_10056 11_10576 11_10327 11_21326 11_20249 11_10772 11_20790 11_20113 11_10726 11_11014 11_10346 11_10721 11_20975 11_10050 11_11098 11_21270 11_20750 11_20671 11_10431 11_20195 11_11122 11_10153 11_10299 11_10924 11_10394 11_20911 11_10073 11_20460 11_20200 11_10055 11_10773 11_21302 11_21335 11_11219 11_11352 11_10370 11_10534 11_21079 11_20349 11_20205 11_10442 11_10531 11_11445 11_20896 11_20230 11_20042 11_20771 11_21409 11_10303 11_20083 11_21201 11_20808 11_20103 11_10169 11_20824 11_20385 11_20092 11_10853 11_20652 11_20570 11_20247 11_11243 11_20354 11_10182 11_21229 11_21209 11_10861 11_21104 11_21160 11_10078 11_10797 11_10454 11_20847 11_10687 11_20139 11_10550 11_21363 11_20452 11_11440 11_11275 11_20962 11_20117 11_20504 11_10999 11_20170 11_20365 11_10174
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RowRowRow HdHdHdHdHd HtHtHt SlSlSl GEarGEarGEar GEarGEar TGWTGW GareaGarea GWidthGWidth GWidth GlengthGlengthGlength W_l PCPCPC SCSCSCSCSCSC PMfldPMfldPMfld PMdla PMdlaPMdla
7H
85
4 Discussion
Genome wide association (GWA) is a powerful approach to dissect and unravel the genetic architecture of complex agronomic traits. The direct utilization of available natural variation for QTL discovery in GWAS has many inherent advantages. LD mapping saves time required for establishment of mapping population which is several years in case of biparental mapping populations. However association mapping populations has to be purified by single seed descent method (SSD) and requires also time. Nevertheless association mapping has more advantage over the biparental mapping as it can be immediately adopted using pure lines. High genetic resolution can be obtained using LD mapping approaches (Rafalski 2010). It is based on many generations of recombination in the ancestral population in comparison to only few recombination events in biparental mapping. The LD decay is variable in different germplasm sets and can be exploited in discovering the QTL at minimum to high resolution (Aranzana et al.
2005; Brachi et al. 2010; Cockram et al. 2010; Morrell et al. 2005; Pasam et al. 2012; Stracke et al. 2007). GWAS in crop plants is challenging as in many cases phenotyping large collections is limiting due to the long life cycle of crop plants. Barley with large and highly repetitive genome is difficult crop to work with at genomic level. However, the recent advances in barley genomics and the establishment of vast genetic resources has opened up the feasibility of gene cloning both by employing mixed strategies map based approaches that include the use of information from sequenced model and crop genomes and GWAS (Close et al. 2009; Komatsuda et al. 2007;
Mayer et al. 2011; Ramsay et al. 2011; Sato et al. 2009). The availability of a large number of SNPs from exonic regions and the recently developed parallel SNP genotyping platforms in barley has incited several GWAS both for gene cloning and QTL detection (Cockram et al. 2010;
Comadran et al. 2011a; Pasam et al. 2012; Schmalenbach et al. 2011). Barley is a predominantly self pollinating diploid species and has high LD blocks and few hundred markers in LD are enough to cover all the barley genome (Brown et al. 1978; Rostoks et al. 2006). Conversely, QTL discovered in high LD germplasm have low genetic resolution as the causal gene could be far from the associated SNP marker. In recent studies, different gene pools of barley were shown to have different LD pattern and the discriminatory LD can be used to fine map QTL and locate candidate genes (Comadran et al. 2011a; Morrell et al. 2005; Russell et al. 2011).
Discussion
86
In the present study, different gene pools were investigated at a genome wide level to discover marker associations for agronomic and biotic stress related traits. The discriminatory LD pattern of these gene pools was exploited in marker associations for the studied traits. Although several marker trait associations were detected in the gene pools, the idea of exploiting the discriminatory LD of gene pools to discover candidate gene has not worked as anticipated in the beginning of the study. Ascertainment bias of the SNP markers was the major problem while comparing associations across the gene pools. Furthermore, in some cases phenotyping of agronomic traits was not possible in all gene pools e.g. wild barley was not studied for the agronomic traits as it was very difficult and time consuming to propagate and work on it.
Similarly landraces from Syria and Jordan were not adapted to the growing conditions of Europe.
As a result only powdery mildew resistance under detached leaf assay was scored on wild barley and landraces under green house growing conditions. Although they were planted twice in the field but they turn out to be complete failures. During the year 2009 LRC were planted during spring but were unable to flower in two locations in Germany (IPK and Halle) (Fig 4.1a). We thought they need vernalization as they originated from Syria and Jordan where they need cold environment during their development. In order to have uniform growth and heading all LRC were planted in winter in the subsequent year 2010. It was too cold for them and most of them were unable to survive under extreme cold conditions of 2010 (Fig 4.1b).
Discussion
87
Fig 4.1: LRC field plots from IPK location; (a) shows heading in Jordanian genotypes and only vegetative growth in Syrian landraces from spring sowing in year 2009 IPK (b) shows complete frost damage during winter in year 2010 IPK