Date of Graduation


Document Type


Degree Name

Doctor of Philosophy in Crop, Soil & Environmental Sciences (PhD)

Degree Level



Crop, Soil & Environmental Sciences


Andy Pereira

Committee Member

Karen A. Moldenhauer

Second Committee Member

Derrick M. Oosterhuis

Third Committee Member

Edward E. Gbur

Fourth Committee Member

Xueyan Sha

Fifth Committee Member

Ainong Shi


Drought stress, Genome-wide association analysis, Genotypes, Meta-QTL analysis, Rice, Water use efficiency


Rice, the second largest staple food crop, uses 30% of global fresh water to complete its life cycle worldwide. Water deficits worldwide have become a serious problem affecting rice growth and ultimately grain yield. To solve the water problem globally, improvement of water use efficiency (WUE) and other drought resistance (DR) traits in rice genotypes would be a useful strategy using advanced genomics tools. In this study, our objectives were to 1) analyze phenotypes of the USDA rice mini-core collection (URMC) for WUE and DR related traits, 2) correlate drought response phenes for physiological traits and grain yield in the URMC, 3) utilize molecular genetic dissection of WUE and DR using genome-wide association (GWA) analysis in the URMC, and 4) conduct genome-wide meta-analysis of QTLs for DR traits and grain yield components under drought stress. In the results, 35 rice genotypes showing ≤25% reduction, 14 rice genotypes exhibiting 25-40% reduction, and 8 rice genotypes showing ≥40% reduction, were drought resistant, moderate drought resistant, and drought-sensitive for WUE, photosynthesis, biomass, and other DR traits under drought stress, respectively. The results suggest from the correlation analysis that strong correlation exists between major grain yield components (number of spikelets per panicle, number of filled and unfilled grains per panicle) and major morpho-physiological traits (plant biomass, photosynthesis, and WUEi). In the GWA analysis, 24, 16, 26, 10, 19, 23, 7, 17, 11, 14, 17, 15, 29, 12, 18, and 19 significant SNPs were highly associated with WUEi, TR, stomatal conductance, Ci & Ci/Ca , plant biomass, NOTs, RWC, LR, chlorophyll content, and chlorophyll fluorescence (Fv’, Fm’, Fv’/Fm’, PhiPSII, ETR, and qN) and their identified candidate genes for WUEi and DR traits. In the meta-analysis, 13 genome-wide MQTLs were found useful containing higher number of QTLs, lower genetic distance with lower CI. Therefore, this information would be useful for the breeding community and geneticists to dissect the genetic architecture of WUE and DR traits for developing high yielding drought resistant rice genotypes.


The supplemental files are supplementary tables that are discussed within this dissertation.

Supplementary Table 4-1.csv (3 kB)
Table 4-1

Supplementary Table 4-2.csv (3 kB)
Table 4-2

Supplementary Table 4-3.csv (5 kB)
Table 4-3

Supplementary Table 4-4.csv (1 kB)
Table 4-4

Supplementary Table 4-5.csv (3 kB)
Table 4-5

Supplementary Table 4-6.csv (3 kB)
Table 4-6

Supplementary Table 4-7A.csv (3 kB)
Table 4-7A

Supplementary Table 4-7B.csv (1 kB)
Table 4-7B

Supplementary Table 4-8.csv (3 kB)
Table 4-8

Supplementary Table 4-9A.csv (1 kB)
Table 4-9A

Supplementary Table 4-9B.csv (2 kB)
Table 4-9B

Supplementary Table 4-10.csv (3 kB)
Table 4-10

Supplementary Table 4-11.csv (2 kB)
Table 4-11

Supplementary Table 4-12.csv (4 kB)
Table 4-12

Supplementary Table 4-13.csv (2 kB)
Table 4-13

Supplementary Table 4-14.csv (2 kB)
Table 4-14

Supplementary Table 4-15.csv (3 kB)
Table 4-15

Supplementary Table 5-1.csv (199 kB)
Table 5-1