Assessing the genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] germplasm collections using phenotypic traits and SNP markers

doi:10.21203/rs.3.rs-26693/v2

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Assessing the genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] germplasm collections using phenotypic traits and SNP markers

https://doi.org/10.21203/rs.3.rs-26693/v2

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published 18 Sep, 2020

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Background: Productivity of cowpea [Vigna unguiculata (L.) Walp] in sub-Sahara Africa is curtailed by a lack of farmer-preferred and improved cultivars and modern production technologies. The objectives of the study were to determine the extent of genetic diversity present among a collection of cowpea accessions from Zambia and Malawi using phenotypic traits and single nucleotide polymorphism (SNP) markers and, to select distinct and complementary parental lines for cultivar development. One hundred cowpea genotypes were evaluated for agronomic traits in two selected sites in Zambia, using a 10×10 alpha lattice design with two replications. Ninety-four of the test genotypes were profiled with 14,116 SNP markers.

Results: Number of pods plant^-1(NPP), pod length (PDL), and number of seeds pod^-1(NSP), were significantly (p<0.05) affected by genotype × environment interaction effects. Genotypes such as CP411, CP421, CP645, CP732, Chimponongo, and MS1-8-1-4 exhibited higher grain yield of > 1200 kg/ha with excellent performance in yield components such as NSP, PDL, HSW and GYD. Grain yield had significant (p<0.05) associations with NPP(r=0.50), NSP (r=0.46) and PDL (r=0.42) useful for simultaneous selection for yield improvement in cowpea. The SNP markers revealed gene diversity and polymorphic information content of 0.22 and 0.17, respectively, showing that the tested cowpea accessions were genetically diverse. Test genotypes were classified into four genetic groups irrespective of source of collection allowing selection and subsequent crosses to develop breeding populations for cultivar development.

Conclusions: Genotypes Bubebe, CP411, CP421, CP645, Chimponogo and MS1-8-1-4 were identified to be the most genetically divergent and high yielding making them ideal parental lines for breeding. This study provided a baseline information and identified promising cowpea genetic resources for effective breeding and systematic conservation.

Population Genetics

Medical Genetics

Molecular Genetics

cowpea

genotypic diversity

phenotypic traits

SNP makers

population structure

yield components

Zambia

Table 1. Qualitative and quantitative traits of cowpea assessed during the study.

No	Trait	Abbreviation	Trait description
Qualitative traits
1	Flower colour	FLC	Flower colour intensity: violet-1, yellow -2, white- 3
2	Leaf green colour	LGC	Colour intensity: light-1, medium -2, dark- 3
3	Growth pattern	GTH	Type 1 - determinant, type 2- indeterminate, type 3- creeping
4	Pod colour	PDC	Pod colour intensity; light green-1, deep green -2, purple- 3
5	Seed coat colour	STC	Primary colour intensity of the seed coat; reddish- brown -1, white -2, purplish- brown -3, brown - 4, black - 5,
6	Leaf size	LFS	Size of the most tip leaf ; small -1, medium -2, big -3
Quantitative traits
1	Days to 50% flowering	DTF	The number of days from sowing until 50% of the plants in a plot have visible flowers
2	Days to 90% maturity	DTM	Days from date of sowing to the date when 90% of pods in a plot turn yellowish brown
3	Number of pods per plant	NPP	Mean number of mature pods from 10 randomly selected and tagged plants in a plot
4	Pod length	PDL	Mean length of 10 mature pods from randomly selected and tagged plants
5	Number of seeds per pod	NSP	Mean weight of seed from mature pods of 10 randomly selected and tagged plants
6	Seed size	SDS	Mean length of 10 randomly selected seed measured in millimetres
7	Hundred seed weight	HSW	Weight of one hundred randomly selected seeds of a genotype measured in grams
8	Grain yield	GYD	The average grain yield per plot and converted into kg ha^-1 using the formula given above.

Table 2. Mean squares and significant tests among 100 cowpea germplasm collections evaluated based on eight quantitative agronomic traits in two locations in Zambia.

Source of variation	DF	DTF	DTM	PDL	NPP	NSP	SDS	HSW	GYD
Location (L)	1	702.20*	13806.30***	542.61***	2550.25***	29.7	0.01	6.30	107770.00
Rep(R)	2	8.30	1731.08***	56.94**	20.91	1.72	2.40	0.67	388357.00
Block (B)	18	196.90	167.30	8.84	61.44	14.77*	5.09*	13.25*	1070734.00***
Genotype (G)	99	242.50*	154.70*	14.02*	64.44	11.93*	2.10	10.26*	532280.00***
Genotype × location	99	161.00	124.30	15.13*	71.32*	11.24*	1.06	8.15	233499.00
Residual	180	148.00	107.20	10.66	50.41	8.66	1.72	7.07	207464.00
Total	399	177.60	168.40	14.08	65.69	10.41	1.80	8.38	334119.00

Note: *, **,*** = Significance at 10%, 5% and 1%, respectively; ns = not significant; DF: degrees of freedom; DTF: days to flowering; DTM: days to maturity; PDL: pod length (cm), NPP: number of pods per plant; NSP: number of seeds per pod, SDS: seed size; HSW: hundred seed weight (g) and GYD: grain yield in kg per hectare

Table 3. Mean values for grain yield and yield components of 100 cowpea genotypes showing the top 10 and bottom 5 ranked genotypes based on grain yield (kg/ha) when assessed in two locations in Zambia

Genotype	DTF	DTM	PDL	NPP	NSP	SDS	HSW	GYD
Top 10 genotypes
CP411	34.50	73.75	20.15	32.25	16.50	3.00	13.48	2197.70
Chimponongo	51.50	79.50	19.52	26.75	16.75	5.00	20.95	2093.20
CP645	51.00	73.25	20.68	28.00	17.25	4.50	13.48	1899.30
MS1-8-1-4	39.75	68.50	21.20	33.25	15.50	5.00	15.03	1779.80
CP732	34.75	81.00	17.02	22.25	16.00	4.50	15.50	1672.40
BB14-16-2-2	36.75	74.00	19.70	25.25	15.50	3.00	11.25	1501.90
ZM3003	39.00	74.50	16.68	18.50	13.50	6.00	14.08	1454.10
CP421	44.75	72.75	19.90	24.00	18.25	3.00	16.23	1328.20
CP2	39.50	75.00	17.53	26.75	16.25	4.50	11.75	1252.70
CP601	40.00	73.50	17.85	22.25	16.75	5.50	13.83	1237.80
Bottom 5 genotypes
ZM2966	38.50	74.50	17.25	18.75	13.75	4.00	13.43	227.10
CP2231	45.75	77.00	15.41	16.75	12.75	6.00	15.13	225.40
ZM2954	47.00	73.75	15.90	19.25	13.50	5.50	14.68	188.20
CP1769	35.25	73.00	18.63	21.25	17.25	5.00	13.55	126.00
ZM6680	29.25	62.75	12.30	16.50	11.25	5.00	15.55	87.00
Mean	41.10	73.86	17.98	21.40	15.60	4.20	12.93	748.56
Minimum	14.00	31.00	6.00	3.00	0.00	3.00	9.10	32.55
Maximum	80.00	96.00	27.20	56.00	24.00	7.00	28.50	5471.24
SE	8.60	7.32	2.31	5.02	2.08	0.92	1.88	322.10
LSD (5%)	16.97	14.50	4.56	9.90	4.11	1.83	3.71	635.50
CV (%)	29.60	14.02	18.16	33.18	18.86	31.09	20.55	60.85

Note: CV: coefficient of variation; LSD: least significant difference; SE: standard error; DTF: days to flowering; DTM: days to maturity; PDL: pod length (UNIT?); NPP: number of pods per plant; NSP: number of seeds per pod; SDS: seed size (mm); HSW: hundred seed weight (g/100 seed); GYD: grain yield in kg ha^-1

Table 4. Estimates of variance components and genetic parameters for yield and yield components among 100 cowpea genotypes evaluated in two locations in Zambia

Component	DTF	DTM	PDL	NPP	NSP	SDS	HSW	GYD
Genotype (G)	21.75	9.27	0.00	0.00	0.42	0.38	0.57	0.10
Location (L)	148.31	125.56	11.10	50.46	8.65	1.78	7.48	0.23
G x L	6.32	0.00	2.01	10.43	1.30	0.00	0.34	0.00
Total (G + L + G x L)	176.38	134.83	13.12	60.89	10.37	2.17	8.39	0.34
Phenotypic variance	61.99	40.66	3.78	17.83	3.23	0.83	2.61	0.16
Heritability (%)	35.00	23.00	0.00	0.00	13.00	46.00	22.00	64.00
GCV (%)	11.35	4.12	0.00	0.00	4.14	14.68	5.82	0.04
PCV (%)	19.16	8.63	10.82	19.73	11.52	21.58	12.48	0.05
GA	5.69	2.99	0.00	0.00	0.48	0.87	0.72	0.53
GA (%)	13.85	4.05	0.00	0.00	3.07	20.58	5.60	0.07

GCV: genotypic coefficient of variation; PCV: phenotypic coefficient of variation; GA: genetic advance; GA (%): genetic advance as a percentage of the mean: DTF: days to flowering; DTM: days to maturity; PDL: pod length; NPP: number of pods per plant; NSP: number of seeds per pod; SDS: Seed Size; HSW: hundred seed weight (g); GYD: grain yield in kg per hectare

Table 5. Correlation coefficients of grain yield and yield components among 100 cowpea genotypes evaluated at two locations in Zambia

Traits	DTF	DTM	PDL	NPP	NSP	SDS	HSWT	GYD
DTF	1
DTM	0.66**	1
PDL	-0.05	0.01	1
NPP	-0.05	-0.05	0.43**	1
NSP	-0.05	0.03	0.64**	0.38**	1
SDS	-0.01	0.00	-0.04	-0.09	-0.30**	1
HSW	0.01	-0.06	0.07	-0.09	-0.12	0.51***	1
GYD	-0.05	-0.07	0.42**	0.50**	0.46**	-0.12	0.04	1

Note: **.*** = Significant at 5% and 1% respectively; DTF: days to flowering; DTM: days to maturity; PDL: pod length (cm), NPP: number of pods per plant; NSP: number of seeds per pod, HSW: hundred seed weight (g), GYD: grain yield in kg per hectare

Table 6. Eigen values, variances and loading scores of eight quantitative traits among 100 cowpea genotypes assessed in two locations in Zambia

Traits	PC1	PC2	PC3
Eigen-values	2.52	1.68	1.50
Proportion variance (%)	31.49	20.97	18.78
Cumulative variance (%)	31.49	52.46	71.25
DTF	-0.09	0.88	-0.22
DTM	-0.03	0.87	-0.27
PDL	0.84	0.06	0.04
NPP	0.72	0.02	0.13
NSP	0.82	-0.01	-0.21
SDS	-0.25	0.18	0.78
HSW	0.02	0.31	0.80
GYD	0.75	0.11	0.27

DTF: days to flowering; DTM: days to maturity; PDL: pod length (cm), NPP: number of pods per plant; NSP: number of seeds per pod, HSW: hundred seed weight (g), GYD: grain yield in kg per hectare PC=principal component

Table 7. Genetic parameters of 90 cowpea germplasm collections assessed based on 14,116 SNP markers

Biological type	GD	PIC	MAF	Ho	F
Whole population	0.22	0.17	0.18	0.30	-0.35
Elite lines	0.21	0.17	0.19	0.30	-0.37
Landraces	0.22	0.18	0.22	0.23	-0.34
Mutant lines	0.26	0.21	0.18	0.35	-0.35
Range	0-0.5	0-0.38	0-0.5	0.25-0.36	-0.52 - -0.13

GD, genetic diversity; PIC, polymorphic information content; MAF, minor allele frequency, Ho, observed heterozygosity; F, inbreeding coefficient

Table 8. Analysis of molecular variance involving 90 cowpea accession based on source of collection

Source	Df	SS	MS	Estimated Variance.	Proportion of variance
Among Populations	2	45.57	22.78	0.54	8%
Within Populations	82	537.96	6.56	6.40	92%
Total	84	583.53		6.95

Df=degrees of freedom, SS=sum of squares, MS=mean squares

Table 9. Genetic differentiation (Fst) and inbreeding coefficients (Fis) among elite lines, landraces and mutant lines of cowpea evaluated in this study

Populations	Inbreeding coefficient (Fst)
	G1	G2	G3
G1	-	0.006	0.012
G2	-0.364	-	-0.004
G3	-0.374	-0.351	-
	Genetic differentiation (Fis)

G1 includes all breeding elite lines, G2 is comprised of landraces collected from farmers in Zambia, G3 consists of mutant lines

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Assessing the genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] germplasm collections using phenotypic traits and SNP markers

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