Fig 1.
Development of the IB population.
Huanghuazhan (HHZ) was used as the recurrent parent and eight diverse varieties as the donor parents. HY, DT, ST and SUT represent high yield under irrigated condition, drought tolerance, salt tolerance and submergence tolerance, respectively.
Table 1.
Details of field experiments.
Fig 2.
Principal component analysis of the IB population and its parents.
The first and the second principal components (PC) are shown as x- and y-axis, respectively. Percentages in brackets denote the variance explained by the respective PC. Donors and IB lines are color-coded based on donor’s geographical origins.
Table 2.
Cold tolerance of the eight families of the IB population and genomic similarities between HHZ and donors.
Fig 3.
Histogram depicting distribution of spikelet fertilities (SF) of the main panicles IB population and the recurrent parent (HHZ) in four cold stress environments.
SF of HHZ is shown with black arrows pointing to the environments.
Table 3.
SF of the IB population and the recurrent parent (HHZ) under four test environments.
Fig 4.
Quantile-quantile plots of cold tolerance tested in four environments.
Yellow, green, blue and red are for XD2013, YX2013, XD2014 and SM2014, respectively.
Fig 5.
Manhattan plot of mixed linear model analysis for cold tolerance.
The letters A, B, C and D indicated XD2013, YX2014, XD2014 and SM2014, respectively.
Table 4.
QTLs identified by GWAS approach under four cold stress environments.
Fig 6.
The physical location of qCT-3-2.
The black colored strip represents chromosome 3 while the grey and white strips indicated the homozygous genotypes of the donor and recurrent parent, respectively. Allele frequency indicated percentage of the alleles derived from HHZ comparing with the entire genome. The phenotypic differences between seven lines were statistically tested using the multiple t-test with Bonferroni adjustment.