Genetic differentiation of grain, fodder and pod vegetable type cowpeas (Vigna unguiculata L.) identified through single nucleotide polymorphisms from genotyping-by-sequencing

Wu, Xingbo; Cortés, Andrés J.; Blair, Matthew W.

doi:10.1186/s43897-022-00028-x

Table 2 Summary of peaks of relative differentiation (based on the average F_ST score)

From: Genetic differentiation of grain, fodder and pod vegetable type cowpeas (Vigna unguiculata L.) identified through single nucleotide polymorphisms from genotyping-by-sequencing

Pairwise comparison	Chromosome	Start (bp)	End (bp)	Length (bp)	Mean FST	Flanking region	Genes	Known QTL
Grain vs. Vegetable	Vu02	24,602,281	24,602,470	189	0.87	24,552,281–24,652,281	9
	Vu03	7,433,261	7,433,390	129	0.87	7,383,261–7,483,261	11
	Vu03	13,546,721	13,547,040	319	0.89	13,496,721–13,596,721	9
	Vu03	13,619,671	13,619,860	189	0.90	13,569,671–13,669,671	7
	Vu03	13,785,361	13,785,590	229	0.88	13,735,361–13,835,361	6
	Vu03	13,793,301	13,793,510	209	0.88	13,743,301–13,843,301	4
	Vu03	13,795,501	13,795,770	269	0.88	13,745,501–13,845,501	4
	Vu03	14,389,911	14,390,100	189	0.90	14,339,911–14,439,911	10
	Vu03	14,571,291	14,571,480	189	0.89	14,521,291–14,621,291	8
	Vu04	2,898,691	2,898,880	189	0.87	2,848,691–2,948,691	10
	Vu06	20,197,641	20,197,830	189	0.87	20,147,641–20,247,641	11
	Vu06	22,810,701	22,810,890	189	0.87	22,760,701–22,860,701	12
	Vu06	23,226,891	23,227,080	189	0.90	23,176,891–23,276,891	15
	Vu06	23,349,871	23,350,000	129	0.93	23,299,871–23,399,871	12
	Vu08	32,138,851	32,139,040	189	0.90	32,088,851–32,188,851	14
	Vu08	33,036,301	33,036,620	319	0.93	32,986,301–33,086,301	13
	Vu08	33,073,211	33,073,310	99	0.92	33,023,211–33,123,211	8
	Vu08	33,103,051	33,103,240	189	0.91	33,053,051–33,153,051	10
	Vu08	33,264,011	33,264,200	189	0.91	33,214,011–33,314,011	14
	Vu08	33,278,221	33,278,410	189	0.87	33,228,221–33,328,221	15
	Vu08	36,035,191	36,035,380	189	0.89	35,985,191–36,085,191	20	Pod length⁴²
	Vu10	33,225,011	33,225,200	189	0.93	33,175,011–33,275,011	11	Seed coat pattern⁴¹
	Vu10	33,226,961	33,227,280	319	0.91	33,176,961–33,276,961	12	Seed coat pattern⁴¹
	Vu10	36,476,061	36,476,250	189	0.88	36,426,061–36,526,061	9	Seed coat pattern⁴¹
	Vu10	36,693,191	36,693,400	209	0.93	36,643,191–36,743,191	11	Seed coat pattern⁴¹
	Vu11	23,872,761	23,872,950	189	0.88	23,822,761–23,922,761	6	Flower scent⁴²
	Vu11	26,358,441	26,358,630	189	0.87	26,308,441–26,408,441	5	Flower scent⁴²
Vegetable vs. Fodder	Vu03	14,561,131	14,561,290	159	0.87	14,511,131–14,611,131	7
	Vu09	15,507,411	15,507,600	189	0.90	15,457,411–15,557,411	5	Seed coat pattern⁴²
	Vu09	16,061,581	16,061,770	189	0.89	16,011,581–16,111,581	4	Seed coat pattern⁴²
	Vu09	16,189,361	16,189,550	189	0.88	16,139,361–16,239,361	1	Seed coat pattern⁴²

Table footnote: Flanking regions, candidate genes, and known QTLs are shown among different subspecies of cowpea. Columns start, end and length correspond to the peaks of divergence, mapped according to the midpoints of consecutive outlier windows, while the flanking region corresponds to the entire 100 kb flanking window surrounding the peak of divergence. The gene search is carried out in the latter.

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ISSN: 2730-9401

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