Identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan

Agre, Paterne A.; Norman, Prince E.; Asiedu, Robert; Asfaw, Asrat

doi:10.1186/s12870-021-03314-w

Table 3 Frequencies and marker prediction effects of various haplotypes associated with tuber yield (kg plant^-1) and reaction to yam mosaic virus infection (AUDPC value)

From: Identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan

Traits	Markers	Hap	Seq	Freq	Adjusted probability	Prob. Adj. significance
Yield	chr04_6236404	Hap1	CCCT	0.475	3.74 e^-05	****
		Hap2	CCTT	0.296	7.11 e^-07	****
		Hap3	CTTT	0.228	0.001	***
	chr04_8196378	Hap1	CCCT	0.481	0.218	ns
		Hap2	CCTT	0.364	0.041	*
		Hap3	CTTT	0.154	0.218	ns
	chr04_18269860	Hap1	AAAC	0.328	0.399	ns
		Hap2	AACC	0.359	0.814	ns
		Hap3	ACCC	0.312	0.814	ns
	chr04_23401186	Hap1	AAAG	0.274	0.029	*
		Hap2	AAGG	0.396	0.001	***
		Hap3	AGGG	0.330	0.619	ns
	chr05_24237388	Hap1	CCCT	0.367	0.020	*
		Hap2	CCTT	0.316	3.57 e^-11	****
		Hap3	CTTT	0.317	1.02 e^-05	****
	chr05_24682916	Hap1	AAAC	0.295	0.921	ns
		Hap2	AACC	0.305	0.044	*
		Hap3	ACCC	0.400	0.043	*
	chr08_7046574	Hap1	AAAC	0.142	0.294	ns
		Hap2	AACC	0.423	1.25 e^-11	****
		Hap3	ACCC	0.435	2.16 e^-08	****
	chr08_10135940	Hap1	CCCG	0.217	0.363	ns
		Hap2	CCGG	0.326	0.522	ns
		Hap3	CGGG	0.457	0.522	ns
	chr10_1317508	Hap1	CCCT	0.363	0.079	ns
		Hap2	CCTT	0.359	0.713	ns
		Hap3	CTTT	0.278	0.246	ns
	chr10_1571815	Hap1	CCCT	0.144	0.873	ns
		Hap2	CCTT	0.362	0.873	ns
		Hap3	CTTT	0.494	0.978	ns
	chr13_13467988	Hap1	CCCT	0.364	0.912	ns
		Hap2	CCTT	0.365	6.12 e^-04	***
		Hap3	CTTT	0.270	0.001	***
	chr14_11301309	Hap1	AAAG	0.110	0.705	ns
		Hap2	AAGG	0.393	0.386	ns
		Hap3	AGGG	0.498	1.01 e^-20	****
	chr14_11128124	Hap1	CCGG	0.414	6.59 e^-18	****
	chr15_5858214	Hap1	CCCT	0.394	0.003	**
		Hap2	CCTT	0.192	0.242	ns
		Hap3	CTTT	0.315	0.057	ns
	chr17_15363223	Hap1	AAAT	0.539	1.20 e^-13	****
Yield	chr17_19041958	Hap1	CCCT	0.146	0.516	ns
		Hap2	CCTT	0.281	0.516	ns
		Hap3	CTTT	0.370	0.799	ns
	chr19_9446619	Hap1	AAAG	0.349	0.002	**
		Hap2	AAGG	0.513	2.94 e^-06	****
		Hap3	AGGG	0.059	0.872	ns
YMV	chr03_6338751	Hap1	GGGT	0.427	1.000	ns
		Hap2	GGTT	0.320	1.000	ns
		Hap3	GTTT	0.466	1.000	ns
	chr10_1116193	Hap1	AAAG	0.226	0.254	ns
		Hap2	AAGG	0.309	0.003	**
		Hap3	AGGG	0.465	6.75 e^-07	****
	chr15_3906069	Hap1	AAAC	0.214	0.882	ns
		Hap2	AACC	0.281	0.882	ns
		Hap3	ACCC	0.412	0.882	ns
	chr16_1482029	Hap1	AAAT	0.307	0.096	ns
		Hap2	AATT	0.424	2.01 e^-04	***
		Hap3	ATTT	0.576	0.006	**
	chr05_30671001	Hap1	AAAG	0.365	1.000	ns
		Hap2	AAGG	0.265	1.000	ns
		Hap3	AGGG	0.369	1.000	ns

ns=non-significant, *, **, ***, and **** indicate significant association between haplotypes and markers

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