class: center, middle, inverse, title-slide # Assessing variability and association of rice agronomic traits across subpopulations and regions ### Uzezi Okinedo ### 12/18/2020 ---  --- class: inverse, middle, center # Introduction --- # Background - A major staple food for an estimated 66% of people in almost all regions  - Predictions have shown that, 60% more rice will have to be produced by 2030 --- # Research problem -- - Although test weight and spikelets per unit area may be the popular predictors of yield, it is highly dependent on on other traits or latent factors. -- - Therefore, it is of relative importance to explore latent factors that might influence test weight across different rice sub-populations and regions in order to improve yield. --- # Aim -- - **i)** To explore trait variation across sub-populations and regions. -- - **ii)** To examine the extent of association between test weight (100 seed weight) and yield attributing traits across rice sub-populations and geographical regions. -- - **iii)** Identify direct and latent factors influencing test weight across sub-populations. --- class: inverse, middle, center # Materials and Methods --- # Rice Diversity Panel 1 Dataset -- - RDP1 (Reg. No. MP-6, NSL 500357 MAP) dataset. - 421 purified homozygous rice (_Oryza sativa_ L.) accessions (GSOR 301001 through GSOR 301421; GSOR 312001 through 312020) including landraces and elite rice cultivars [Dataset](https://www.ars.usda.gov/ARSUserFiles/60280500/RDP1/RDP1_JPR%20pheno%20and%20marker%20data%20for%20submission%20to%20GSOR-GRIN_v6_R2_08042016.xlsx). -- Six sub-population groups namely; Indica (IND), Aus (AUS), Tropical japonica (TRJ), Temperate japonica (TEJ), Aromatic (ARO), Admixed (ADMIX) --- # Statistical Analysis -- - **Standardized major axis (SMA) slopes** for bivariate trait relationships summary and significance test of trait associations -- - **Structural Equation Model (SEM)** for structural relationship evaluation and estimation of interrelated dependence -- - Linear regression to predict test weight --- class: inverse, middle, center # Results --- # Data Exploration <img src="PRESENTATION_OKINEDO_UZEZI_2020_files/figure-html/unnamed-chunk-1-1.png" width="80%" style="display: block; margin: auto;" /> --- <img src="PRESENTATION_OKINEDO_UZEZI_2020_files/figure-html/unnamed-chunk-2-1.png" width="80%" style="display: block; margin: auto;" /> --- <img src="PRESENTATION_OKINEDO_UZEZI_2020_files/figure-html/unnamed-chunk-3-1.png" width="80%" style="display: block; margin: auto;" /> --- --- # SMA Regression across subpopulations <img src="PRESENTATION_OKINEDO_UZEZI_2020_files/figure-html/unnamed-chunk-4-1.png" width="80%" style="display: block; margin: auto;" /> --- ```r # make a facet-wrap to view relationship across groups florets_per_panicle + facet_wrap(~subpopulation, ncol=2) ``` <img src="PRESENTATION_OKINEDO_UZEZI_2020_files/figure-html/echo FALSE-1.png" width="80%" style="display: block; margin: auto;" /> --- # SMA Summary for Total Florets per panicle association across subpopulations <div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:350px; overflow-x: scroll; width:700px; "><table class=" lightable-paper" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; margin-left: auto; margin-right: auto;'> <thead> <tr> <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> group </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> n </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> r2 </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> pval </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Slope </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Slope_lowCI </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Slope_highCI </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Int </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Int_lowCI </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Int_highCI </th> <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Slope_test </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Slope_test_p </th> <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Elev_test </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Elev_test_p </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> ADMIX </td> <td style="text-align:right;"> 56 </td> <td style="text-align:right;"> 0.1613282 </td> <td style="text-align:right;"> 0.0021530 </td> <td style="text-align:right;"> -1.0019881 </td> <td style="text-align:right;"> -1.2831417 </td> <td style="text-align:right;"> -0.7824390 </td> <td style="text-align:right;"> 0.4253753 </td> <td style="text-align:right;"> 0.1263962 </td> <td style="text-align:right;"> 0.7243544 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> ARO </td> <td style="text-align:right;"> 7 </td> <td style="text-align:right;"> 0.3560280 </td> <td style="text-align:right;"> 0.1572758 </td> <td style="text-align:right;"> -3.3027580 </td> <td style="text-align:right;"> -7.5404121 </td> <td style="text-align:right;"> -1.4466332 </td> <td style="text-align:right;"> -2.9293795 </td> <td style="text-align:right;"> -5.4986269 </td> <td style="text-align:right;"> -0.3601320 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> AUS </td> <td style="text-align:right;"> 51 </td> <td style="text-align:right;"> 0.0767219 </td> <td style="text-align:right;"> 0.0490988 </td> <td style="text-align:right;"> -0.7737894 </td> <td style="text-align:right;"> -1.0161392 </td> <td style="text-align:right;"> -0.5892401 </td> <td style="text-align:right;"> -0.8708629 </td> <td style="text-align:right;"> -1.1211628 </td> <td style="text-align:right;"> -0.6205630 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> IND </td> <td style="text-align:right;"> 73 </td> <td style="text-align:right;"> 0.0280656 </td> <td style="text-align:right;"> 0.1565744 </td> <td style="text-align:right;"> -0.8576659 </td> <td style="text-align:right;"> -1.0807839 </td> <td style="text-align:right;"> -0.6806086 </td> <td style="text-align:right;"> -0.5036280 </td> <td style="text-align:right;"> -0.7507534 </td> <td style="text-align:right;"> -0.2565026 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> TEJ </td> <td style="text-align:right;"> 92 </td> <td style="text-align:right;"> 0.0000873 </td> <td style="text-align:right;"> 0.9295503 </td> <td style="text-align:right;"> 1.0138130 </td> <td style="text-align:right;"> 0.8235053 </td> <td style="text-align:right;"> 1.2480998 </td> <td style="text-align:right;"> 0.8539348 </td> <td style="text-align:right;"> 0.5901924 </td> <td style="text-align:right;"> 1.1176772 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> TRJ </td> <td style="text-align:right;"> 85 </td> <td style="text-align:right;"> 0.3162021 </td> <td style="text-align:right;"> 0.0000000 </td> <td style="text-align:right;"> -0.9617684 </td> <td style="text-align:right;"> -1.1509440 </td> <td style="text-align:right;"> -0.8036867 </td> <td style="text-align:right;"> 0.8723962 </td> <td style="text-align:right;"> 0.6641858 </td> <td style="text-align:right;"> 1.0806066 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> </tbody> </table></div> --- # SMA across regions -- <img src="PRESENTATION_OKINEDO_UZEZI_2020_files/figure-html/unnamed-chunk-6-1.png" width="80%" style="display: block; margin: auto;" /> --- # Significant associations for Total Florets per panicle across regions -- <div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:350px; overflow-x: scroll; width:700px; "><table class=" lightable-paper" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; margin-left: auto; margin-right: auto;'> <thead> <tr> <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> group </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> n </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> r2 </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> pval </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Slope </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Slope_lowCI </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Slope_highCI </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Int </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Int_lowCI </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Int_highCI </th> <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Slope_test </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Slope_test_p </th> <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Elev_test </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Elev_test_p </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> Africa </td> <td style="text-align:right;"> 37 </td> <td style="text-align:right;"> 0.1824934 </td> <td style="text-align:right;"> 0.0083630 </td> <td style="text-align:right;"> -1.2247427 </td> <td style="text-align:right;"> -1.6623304 </td> <td style="text-align:right;"> -0.9023444 </td> <td style="text-align:right;"> 0.9025426 </td> <td style="text-align:right;"> 0.5346671 </td> <td style="text-align:right;"> 1.2704181 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> Caribbean </td> <td style="text-align:right;"> 6 </td> <td style="text-align:right;"> 0.0058945 </td> <td style="text-align:right;"> 0.8850630 </td> <td style="text-align:right;"> -0.6217080 </td> <td style="text-align:right;"> -1.9221328 </td> <td style="text-align:right;"> -0.2010896 </td> <td style="text-align:right;"> 0.4849523 </td> <td style="text-align:right;"> -0.2637442 </td> <td style="text-align:right;"> 1.2336489 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> Central America </td> <td style="text-align:right;"> 6 </td> <td style="text-align:right;"> 0.5675139 </td> <td style="text-align:right;"> 0.0837613 </td> <td style="text-align:right;"> -0.9795673 </td> <td style="text-align:right;"> -2.2206821 </td> <td style="text-align:right;"> -0.4320979 </td> <td style="text-align:right;"> 0.7868129 </td> <td style="text-align:right;"> 0.2336541 </td> <td style="text-align:right;"> 1.3399717 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> Central Asia </td> <td style="text-align:right;"> 6 </td> <td style="text-align:right;"> 0.2078680 </td> <td style="text-align:right;"> 0.3634980 </td> <td style="text-align:right;"> -0.9024660 </td> <td style="text-align:right;"> -2.5495213 </td> <td style="text-align:right;"> -0.3194501 </td> <td style="text-align:right;"> -0.7732753 </td> <td style="text-align:right;"> -1.9320294 </td> <td style="text-align:right;"> 0.3854787 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> East Asia </td> <td style="text-align:right;"> 74 </td> <td style="text-align:right;"> 0.0000042 </td> <td style="text-align:right;"> 0.9862292 </td> <td style="text-align:right;"> -0.8872140 </td> <td style="text-align:right;"> -1.1198035 </td> <td style="text-align:right;"> -0.7029346 </td> <td style="text-align:right;"> -0.3062358 </td> <td style="text-align:right;"> -0.5754577 </td> <td style="text-align:right;"> -0.0370139 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> East Europe </td> <td style="text-align:right;"> 15 </td> <td style="text-align:right;"> 0.0024563 </td> <td style="text-align:right;"> 0.8607635 </td> <td style="text-align:right;"> -0.7441415 </td> <td style="text-align:right;"> -1.3125404 </td> <td style="text-align:right;"> -0.4218892 </td> <td style="text-align:right;"> 0.2996701 </td> <td style="text-align:right;"> -0.4128345 </td> <td style="text-align:right;"> 1.0121747 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> North America </td> <td style="text-align:right;"> 43 </td> <td style="text-align:right;"> 0.0952134 </td> <td style="text-align:right;"> 0.0440929 </td> <td style="text-align:right;"> -0.7525207 </td> <td style="text-align:right;"> -1.0114193 </td> <td style="text-align:right;"> -0.5598938 </td> <td style="text-align:right;"> 0.4403637 </td> <td style="text-align:right;"> 0.1625446 </td> <td style="text-align:right;"> 0.7181829 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> Oceania </td> <td style="text-align:right;"> 6 </td> <td style="text-align:right;"> 0.0381806 </td> <td style="text-align:right;"> 0.7106325 </td> <td style="text-align:right;"> -0.9618998 </td> <td style="text-align:right;"> -2.9344850 </td> <td style="text-align:right;"> -0.3153028 </td> <td style="text-align:right;"> -0.3175809 </td> <td style="text-align:right;"> -1.5986496 </td> <td style="text-align:right;"> 0.9634879 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> South America </td> <td style="text-align:right;"> 30 </td> <td style="text-align:right;"> 0.2966206 </td> <td style="text-align:right;"> 0.0018599 </td> <td style="text-align:right;"> -1.2485895 </td> <td style="text-align:right;"> -1.7181157 </td> <td style="text-align:right;"> -0.9073753 </td> <td style="text-align:right;"> 0.2048406 </td> <td style="text-align:right;"> -0.1542327 </td> <td style="text-align:right;"> 0.5639140 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> South Asia </td> <td style="text-align:right;"> 63 </td> <td style="text-align:right;"> 0.0774085 </td> <td style="text-align:right;"> 0.0272509 </td> <td style="text-align:right;"> -0.7995030 </td> <td style="text-align:right;"> -1.0199343 </td> <td style="text-align:right;"> -0.6267120 </td> <td style="text-align:right;"> -0.7127386 </td> <td style="text-align:right;"> -0.9639363 </td> <td style="text-align:right;"> -0.4615409 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> Southeast Asia </td> <td style="text-align:right;"> 46 </td> <td style="text-align:right;"> 0.0531385 </td> <td style="text-align:right;"> 0.1232532 </td> <td style="text-align:right;"> -0.7999274 </td> <td style="text-align:right;"> -1.0706494 </td> <td style="text-align:right;"> -0.5976596 </td> <td style="text-align:right;"> 0.0055228 </td> <td style="text-align:right;"> -0.3641482 </td> <td style="text-align:right;"> 0.3751938 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> West Asia </td> <td style="text-align:right;"> 11 </td> <td style="text-align:right;"> 0.0015596 </td> <td style="text-align:right;"> 0.9082219 </td> <td style="text-align:right;"> 1.0253296 </td> <td style="text-align:right;"> 0.5112472 </td> <td style="text-align:right;"> 2.0563454 </td> <td style="text-align:right;"> 0.9416803 </td> <td style="text-align:right;"> -0.0834793 </td> <td style="text-align:right;"> 1.9668400 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> <tr> <td style="text-align:left;"> West Europe </td> <td style="text-align:right;"> 21 </td> <td style="text-align:right;"> 0.0047711 </td> <td style="text-align:right;"> 0.7660808 </td> <td style="text-align:right;"> -1.0065084 </td> <td style="text-align:right;"> -1.5981729 </td> <td style="text-align:right;"> -0.6338858 </td> <td style="text-align:right;"> 0.8928619 </td> <td style="text-align:right;"> 0.3737050 </td> <td style="text-align:right;"> 1.4120189 </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> <td style="text-align:left;"> NA </td> <td style="text-align:right;"> NA </td> </tr> </tbody> </table></div> --- # Structural Equation Modeling (SEM) <img src="PRESENTATION_OKINEDO_UZEZI_2020_files/figure-html/unnamed-chunk-8-1.png" width="80%" style="display: block; margin: auto;" /> --- # Path Summary -- <div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:350px; overflow-x: scroll; width:700px; "><table class=" lightable-paper" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; margin-left: auto; margin-right: auto;'> <thead> <tr> <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Effect </th> <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> ADMIX </th> <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> ARO </th> <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> AUS </th> <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> IND </th> <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> TEJ </th> <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> TRJ </th> <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Proposed.interpretation </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> FLN_HHG </td> <td style="text-align:left;"> -0.77 </td> <td style="text-align:left;"> -4.88 </td> <td style="text-align:left;"> 0.98 </td> <td style="text-align:left;"> -0.98 </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> -0.61 </td> <td style="text-align:left;"> HHG variation is strongly influenced by FLN; Decreasing FLN increases grain weight except in TEJ </td> </tr> <tr> <td style="text-align:left;"> PNN_HHG </td> <td style="text-align:left;"> -0.44 </td> <td style="text-align:left;"> 0.18 </td> <td style="text-align:left;"> -0.55 </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> -0.42 </td> <td style="text-align:left;"> -0.9 </td> <td style="text-align:left;"> HHG variation is strongly influenced by PNN except in IND </td> </tr> <tr> <td style="text-align:left;"> FGN_HHG </td> <td style="text-align:left;"> -0.42 </td> <td style="text-align:left;"> 1.57 </td> <td style="text-align:left;"> 0.46 </td> <td style="text-align:left;"> 0.71 </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> Increase in filled grain per panicle increases test weight except in TEJ and TRJ </td> </tr> <tr> <td style="text-align:left;"> DTH_PTH </td> <td style="text-align:left;"> -0.46 </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> 0.21 </td> <td style="text-align:left;"> 0.23 </td> <td style="text-align:left;"> There is a relationship between DTH and PTH in ADMIX, TEJ and TRJ, although causality is not asumed </td> </tr> <tr> <td style="text-align:left;"> DTH_FGN </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> -0.41 </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> 0.53 </td> <td style="text-align:left;"> 0.56 </td> <td style="text-align:left;"> DTH either increases or decreses FGN depending on the rice subpopulation </td> </tr> <tr> <td style="text-align:left;"> DTH_PNN </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> Panicle number is not dependent on days to heading </td> </tr> <tr> <td style="text-align:left;"> DTH_FLN </td> <td style="text-align:left;"> 0.5 </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> 0.53 </td> <td style="text-align:left;"> 0.35 </td> <td style="text-align:left;"> DTH regulates FLN </td> </tr> <tr> <td style="text-align:left;"> PTH_FGN </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> PTH controls FGN in AUS </td> </tr> <tr> <td style="text-align:left;"> PTH_FLN </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> 0.5 </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> PTH controls FLN in TEJ </td> </tr> <tr> <td style="text-align:left;"> PTH_PNN </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> -0.35 </td> <td style="text-align:left;"> NS </td> <td style="text-align:left;"> PTH controls PNN in TEJ </td> </tr> </tbody> </table></div> --- # Predicting test weight with total floret number -- <img src="PRESENTATION_OKINEDO_UZEZI_2020_files/figure-html/unnamed-chunk-10-1.png" width="80%" style="display: block; margin: auto;" /> --- class: inverse, middle, center # Summary --- # Key Points - Total florets per panicle has the most significant association - Based on the Root Mean Square Error of Approximation (RMSEA > 0.5) and Standardized Root Mean Square Residual (SRMSR), the model was a good fit for the data. - Plant height is an important in test weight improvement in the Temperate Japonicas - Indirect effect traits like Days to heading affects test weight via floret number and should be fully considered for breeding purposes TEJ and TRJ subpopulations --- class: inverse, middle, center # Thank you! ---