Table 2.

Summary of common candidate loci between hyperspectral results and chalk trait in the mini-core diversity panel.

Chr	Peak SNP (bp)	P	R2	Candidate gene	Description
1	28,782,853	4.86 × 10−7	0.24	LOC_Os01g50060	1-aminocyclopropane-1-carboxylate deaminase
1	31,494,903	1.99 × 10−8	0.26	LOC_Os01g54560 ¤ ‡	Trehalose synthase
3	3,823,250	1.20 × 10−7	0.25	LOC_Os03g07480 ¤ ‡	Sucrose transporter (SUT1)
3	22,433,619	1.84 × 10−8	0.27	LOC_Os03g40270 ¤ ‡	Alpha-1,4-glucan-protein synthase
3	28,376,883	4.58 × 10−7	0.27	LOC_Os03g49800	Phosphatidylinositol-4-phosphate 5-kinase (PIPK)
4	21,277,848	7.00 × 10−7	0.18	LOC_Os04g35030	Cellulose synthase-like protein (CSLH3)
4	22,079,754	4.81 × 10−7	0.24	LOC_Os04g36610 ¤	Endoglucanase
5	3,349,202	3.16 × 10−7	0.29	LOC_Os05g06480	Inorganic H + pyrophosphatase (chalk5)
6	4,719,289	9.52 × 10−8	0.26	LOC_Os06g09450 ¤	Sucrose synthase (SUS2)
8	15,723,764	6.76 × 10−8	0.26	LOC_Os08g25734	Glucose-1-phosphate adenylyltransferase (AGPS2)
10	4,312,440	2.16 × 10−7	0.28	LOC_Os10g08022 ¤ ‡	Fructose-bisphosphate aldolase isozyme

^‡ - denotes candidate loci discussed in discussion.

^¤ - denotes candidate loci associated with grain chalk segments.