AJCS 18(07):401-407 (2024) ISSN:1835-2707

https://doi.org/10.21475/ajcs.24.18.07.p3994

Genetic diversity and population structure of a modified three-way

tomato hybrids for determining fruit size traits

Stephen I. Nnungu*

, Michael I. Uguru

Department of Crop Science, University of Nigeria, Nsukka, Nigeria

Abstract: The assessment of genetic diversity and

genetic structure of crops has a vital impact on the

plant breeding program, including the characterization,

use and conservation of genetic material. The genetic

diversity and genetic structure of a set of 94 F

3

tomato

hybrids were assessed with 25 polymorphic SNP

markers of quantitative trait loci (QTLs) underlying fruit

hybrids. Cluster analysis using the unweighted pair

group method with arithmetic mean methods (UPMA)

consistent with the size, shape and number of locules of

with SNP markers revealed three subpopulations.

Association mapping using 25 SNP markers detected 9

markers with a significant association with mean fruit

weight, fruit length, fruit diameter, number of locules,

and fruit shape index. The nine markers detected in this

study are recommended for the tomato fruit size

improvement breeding program.

Keywords: Genetic diversity, Population structure, SNPs markers,

Tomato (

) is one of the most important local

market vegetables in Nigeria grown by small-scale farmers. Tomato

production is considered as one of the main agricultural enterprises as it

employs people in farms, processing industries and provides higher

income per hectare to small holder farmers than most staple crops

(AVRDC, 2006). However, they are many constraints affect the

The main objectives of current tomato breeding, such as increasing fruit

cultivated genetic resources (Xu et al., 2013). Interpreting patterns of

genetic variability in cultivated landraces of economically important

crops allows breeders to reconsider this trait reservoir and, eventually,

identify new alleles to improve productivity, adaptation, fruit quality and

size, and nutritional value. To date, much of this germplasm has not

been widely characterized and most local varieties have not yet been

used in modern plant breeding (Huang et al., 2010).

The improvement of tomato with an ability to withstand the high

humidity conditions of South Eastern Nigeria impelled the initiation of a

hybridization programme. Crosses between two commercially acceptable

exotic breeds with large fruited inbred (supersteak) which called a

modified three way crosses and the selection from the segregating

population. Successive evaluations of the progenies at different filial

generation from F

1

to F

2

showed reliable evidence of increased fruit yield

particularly in terms of fruit size. Since fruit size is quantitatively

inherited, that mean affected by environment, the molecular markers

analysis is inevitable to confirm the fruit size quantitative trait loci

Successful breeding for crop improvement programmes depends on

2004). Lack of genetic variability may limit breeding progress and gain

from selection (Cornelious and Sneller, 2002). So, knowledge of the

genetic diversity of any germplasm collection provides a basis for

improvement of crops and development of superior cultivars. Detailed

understanding of the population structure and diversity is also needed

for the conservation planning, management and utilization of tomato

germplasm (Hamrick and Godt, 1996; Frankham et al., 2002).

The availability of cost-effective, accurate and rapid genotyping tests

has made single nucleotide polymorphism (SNP) the most frequently

used DNA marker for high-throughput plant analysis, encouraging

molecular markers that have immense significance in plant genetics and

breeding because of their excellent distribution throughout the genome

and suitability for genetic diversity analysis, evolutionary relationships

and genetic population substructure estimation (Rafalski, 2002; Garris et

al., 2003; Varshney et. al., 2008). Therefore, Single Nucleotide

Polymorphisms (SNPs) markers of the quantitative trait loci (QTL)

underlying fruit sizes in tomato were performed in this study. The

determining traits.

Results

The results from 25 SNPs markers used for this work on tomato fruit

size detected appreciable degree of polymorphism within the set of

tomato progenies used for this work. A total of 50 SNPs alleles were

detected and the total number of allele detected per primer was 2. Most

of the loci produced a maximum of two rare alleles. Some of the alleles

may be useful as diagnostic markers for some of the assayed tomato

progenies.

e

o

markers with 0.5 >PIC>0.2 were just considered to be informative

(Bostein et al., 1980). However, because of the bi allelic nature of the

SNPs markers, the maximum PIC value is only 0.5 while SSRs markers

can go beyond 0.5. The variation was significantly associated with the

number of alleles detected at each locus. Therefore, SNPs markers

showed a reasonable amount of variation in the tomato genotypes in this

study.