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Euphytica (2024) 220:2
https://doi.org/10.1007/s10681-023-03257-3
RESEARCH
Uncovering alleles beneficial forseed characteristics
indurum wheat (Triticum durum Desf.) landraces
andcultivars
YoussefChegdali· HassanOuabbou·
AbdelkhalidEssamadi· AliSahri·
SusanneDreisigacker· CarlosGuzmán
Received: 27 April 2023 / Accepted: 22 November 2023
© The Author(s), under exclusive licence to Springer Nature B.V. 2023
polymorphic loci and ten monomorphic loci. The
polymorphic loci were Wx-B1, TaCwi-4A, TaGS5-A1,
and TaSus1-7B. The monomorphic loci included Wx-
A1, TaCwi-A1, TaGW2, TGW6-4A, TaSus1-7A-1185,
TaSus1-7A-1599, TaSus1-7A-3544, TaSus2-2A,
TaSus2-2B, and TGW6. The highest frequencies of
desirable alleles were found in the LAN group, fol-
lowed by MC and NAC. LAN carried the desirable
alleles, Wx-B1b, Hap-4A-T, TaGS5-A1b, and Hap-T,
at the Wx-B1, TaCwi-4A, TaGS5-A1, and TaSus1-
7B loci, respectively. The number of favorable
alleles in each accession was significant, with LAN
accession MGB-3083 carrying up to 12 favorable
alleles. Additionally, four accessions had 11 favora-
ble alleles, namely MC MGB-22, LAN MGB-3101,
and two NAC lines (MGB-66035 and MGB-6606).
Abstract Landraces and ancient cultivars offer the
potential for re-selecting key traits and alleles that
might enhance grain yield. A durum wheat collec-
tion consisting of 18 landraces (LAN), 5 Moroccan
cultivars (MC), and 11 North American cultivars
(NAC) was analyzed for seed characteristics and 14
loci associated with grain weight. The study found
significant genetic variation in seed characteris-
tics, with the NAC and MC cultivars having higher
mean values compared to LAN. Several accessions
displayed promising traits for grain weight and size.
The genotyping results showed that there were four
Supplementary Information The online version
contains supplementary material available at https:// doi.
org/ 10. 1007/ s10681- 023- 03257-3.
Y.Chegdali(*)· H.Ouabbou· A.Sahri
Laboratory ofGene Bank, Crop Physiology andGenetic
Resources, Institut National de la Recherche Agronomique
(INRA), B.P. 589, Settat, Morocco
e-mail: youssefchegdali89@gmail.com
H. Ouabbou
e-mail: hassan.ouabbou@gmail.com
A. Sahri
e-mail: sahriali@gmail.com
Y.Chegdali· A.Essamadi
Laboratory ofBiochemistry andNeuroscience, Naturel
Resources andEnvironnement, Faculty ofSciences
andTechnology, Hassan 1, University, P.O. Box577,
Settat, Morocco
e-mail: essamadi@uhp.ac.ma
S.Dreisigacker
Global Wheat Program, CIMMYT, Km 45 Carretera,
México-Veracruz, El Batán, C.P.56130Texcoco,
EstadodeMéxico, México
e-mail: s.dreisigacker@cgiar.org
C.Guzmán
Departamento de Genética, Escuela Técnica Superior
de Ingeniería Agronómica y de Montes, Edificio Gregor
Mendel, Campus de Rabanales, Universidad de Córdoba,
CeiA3, 14071Córdoba, Spain
e-mail: carlos.guzman@uco.es
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In conclusion, the current study offers insights for
improving durum wheat yield by identifying high
genetic variation among desirable characteristics
and alleles among accessions, as well as highlight-
ing accessions with excellent allele combinations of
important yield-related genes.
Keywords Durum wheat· Seed characteristics·
Favorable alleles· Grain yield
Abbreviations
AACC American Association of Cereal Chemists
CRRA Regional Center for Agricultural Research
CTAB Cetyltrimethylammonium bromide
INRA National Institute for Agricultural Research
KASP Kompetitive allele specific PCR
LAN Landraces
MC Moroccan Cultivars
MGB Moroccan Gene banque
NAC North American cultivars
PCR Polymerase chain reaction
STS Sequence-tagged sites
SNP Single nucleotide polymorphisms
Introduction
Durum Wheat (T. turgidum ssp. durum) is an impor-
tant cereal crop, contributing to food production and
agricultural income. It is cultivated on 13.5 million
hectares (Mha) with a global production of 33.8 mil-
lion tons in 2020/21 (Dahl 2017; IGC 2022). Durum
wheat cultivation is more concentrated in the Medi-
terranean area, which accounts for about 60% of the
durum wheat area globally (Royo et al. 2017). In
terms of area and production, approximately half of
the world’s acreage and production comes from the
Mediterranean countries (Martínez-Moreno et al.
2022). Countries around the Mediterranean are the
largest importers and consumers of durum wheat
products (Xynias etal. 2020). As dominant food crop,
durum wheat is consumed in various forms, such as
bread, couscous, bulgur, freekeh, semolina, and pasta.
Among the countries in this region, Morocco is one
of the largest importers and consumers of durum
wheat. Although its projected production reaches
about 7.5 million quintals (MQx), national produc-
tion struggles to reach self-sufficiency (MAPM-
DREF 2021), with a per capita consumption of about
90 kg (Taghouti et al. 2017). With the impact of
climate change, the projected increase of the gobal
population by 2050, and the reduction in genetic crop
diversity, the Moroccan agricultural sector will have
to adapt to new challenges in order to achieve self-
sufficiency, including for durum wheat. One of the
main approaches to accomplish this goal is the devel-
opment of new high-yielding durum wheat varieties;
e.g., by increasing the availability of genetic diversity
using agro-morphological and molecular characteri-
zation of unexploited durum wheat resources.
To improve durum wheat yield, it is necessary to
improve and maintain the supply of new varieties and
to establish a stable system for securing and supply-
ing excellent seeds. One way to achieve this is, durum
breeders must enrich the current elite gene pool by
reintroducing valuable traits and alleles from lan-
draces and unrelated advanced cultivars. Increasing
genetic diversity in modern durum wheat cultivars
can contribute to enhance durum wheat productivity
(Balla etal. 2022). Large and useful genetic diversity
from durum landraces could help breeding programs
to create new high-yielding varieties by introducing
favorable alleles related to grain yield, e.g., for grain
weight. Sharma etal. (2021) noted that grain weight
and size are among the characteristics that have
been modified during domestication and subsequent
breeding. Uncovering the diversity associated with
thousand kernel weight (TKW) present in landraces
and cultivars provides the possibility of integrat-
ing desired alleles into durum wheat breeding pro-
grams helping ot meet the growing demand for higher
yields.
Assessment of genetic diversity and identifica-
tion of valuable traits and alleles can be based on
agro-morphometric and molecular markers. Agro-
morphometric markers include the use of imaging
analysis to analyze individual seed attributes and
predict flour yield prior to the milling process (Yab-
walo etal. 2018). Seed attributes have also been pre-
dictive of grain specific weight. Many studies have
shown that TKW is significantly associated with
grain dimensions and a predictive model has been
developed (Troccoli and di Fonzo 1999; Novaro etal.
2001; Kim etal. 2021; Assadzadeh etal. 2022). As
TKW is a relatively stable component of wheat yield,
it will be a promising approach to improving durum
wheat yield in wheat breeding programs (Cristina
et al. 2022). Durum wheat grain is also comprised
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of approximately 70% starch content (Koczoń et al.
2022), and a high specific weight is positively corre-
lated with a high starch content. Recent research has
recognized the crucial role of starch in determining
flour quality, dough functionality, nutritional value
and quality, and final product quality (Regina and
Guzmán 2020). As a result, assessing the starch con-
tent can be advantageous.
Molecular marker have become increasingly popu-
lar in recent years to improve the efficiency of charac-
terization, genetic diversity assessment, and selection.
More recent marker technologies include kompeti-
tive allele-specific PCR (KASP) markers utilized for
QTL profiling or marker-assisted selection (Rasheed
et al. 2016; Khalid et al. 2019; Sehgal et al. 2019;
Zhao etal. 2019; Zhang etal. 2021; Chegdali et al.
2022a; Jiao et al. 2023). Khalid et al. (2019) com-
piled a list of loci associated with agronomic char-
acteristics along with their favorable and unfavorable
alleles, including loci related to starch content and
grain weight, making the use of molecular markers
attractive for durum wheat breeding process. One
of the key steps in the breeding process is genotypic
characterization. Therefore, characterization based
on functional markers and their alleles would be ben-
eficial in breeding programs by increasing the use of
unexploited durum wheat genetic resources stored in
genebanks, notably providing accurate information on
favaorable and defavorable alleles for each genotype.
The Regional Agricultural Research Center of
Settat-Morocco maintains a gene bank that contains
more than 3000 accessions of durum wheat. These
accessions consist of ancient and modern Moroccan
cultivars, landraces collected from durum wheat-
producing regions within the country, as well as col-
lections of durum wheat from other countries that
are highly valued by Moroccan farmers and indus-
tries in terms of productivity and quality. However,
many of these collected and preserved genotypes
have not yet been studied for their important agro-
nomic characteristics, particularly in terms of ben-
eficial genes or alleles. To provide durum wheat
breeders with a pool of valuable traits and alleles
for breeding new high-yielding varieties, a sub-col-
lection of durum wheat landraces and advanced cul-
tivars stored at the Moroccan Genebank was char-
acterized using both agronomic characterization
and molecular markers. This characterization was
carried out using seven seed characteristics and 14
functional markers related to grain weight and size
to identify favorable and unfavorable alleles. The
study also aimed to highlight the alleles most use-
ful for improving durum wheat yield in Moroccan
breeding programs.
Material andmethods
Plant materials
Thirty-four accessions were used in this study,
composed of durum wheat landraces and advanced
cultivars, all obtained from the Genebank of the
Regional Center for Agricultural Research (CRRA)
in Settat, which is affiliated with the National Insti-
tute for Agricultural Research (INRA) in Rabat,
Morocco. The accessions were evaluated for supe-
rior grain weight characteristics and desirable
alleles (Supplementary Data Sheet 1). Durum wheat
accessions comprised 18 landraces (LAN) acces-
sions originated from various parts of Morocco,
5 Moroccan cultivars (MC) developed through
INRA’s collaboration with international research
centers and 11 North American cultivars (NAC)
from Canada and the USA. NAC were previously
used as novel genetic resources to enhance grain
yield and grain quality. A list of all the accessions
used in this study can be found in Table1.
Agronomic characterization
Agronomic characterization has focused on seed
characteristics and related traits as important yield-
enhancing parameters in wheat breeding programs.
Starch content (SC, mg/g) was determined using the
methods of Hansen and Møller (1975) and Ashwell
(1957). Seed characteristics were estimated using
the GrainScan digital image software (version 1.
0.140429) as described by Whan et al. (2014). The
characteristics estimated were area (A, mm2), perim-
eter (P, mm), length (L, mm), and width (mm). The
seed size values represent an average measurement
from twenty seeds. Thousand kernel weight (TKW,
g) and specific weight (SW, kg/hl) were determined
according to the American Association of Cereal
Chemists (AACC) 55-10 (AACC 2000).
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Genotypic characterization
Genotypic characterization was used to identify desir-
able and undesirable alleles related to grain weight in
each accession, as well as their distribution across the
entire collection and among the three studied groups.
Genomic DNA of the 34 accessions was isolated from
young seedlings using the modified CTAB method
described in the laboratory manual of Dreisigacker
et al. (2016). The extracted DNA was quantified
using the NanoDrop 8000 spectrophotometer (ver-
sion 2.1.0) from Thermo Fischer Scientific. Genotyp-
ing was performed using 14 markers, including two
Sequence-Tagged Sites (STS) and 12 Single Nucleo-
tide Polymorphisms (SNP) markers, to evaluate the
QTL profile and frequency distribution of favorable
and unfavorable alleles of the accessions and among
groups (Supplementary Data Sheet 2).
For STS marker genotyping, the reaction mixture
for polymerase chain reaction (PCR) amplification
was prepared in a final volume of 10µl and contained
1X Green Go-Taq, 1.5mM MgCl2, 200 µM dNTPs,
0.25 µM each of Primers F and R, 0.25U DNA
Polymerase (Go-Taq®Flexi, Promega, USA, Cat. #
M8295), and 46ng of genomic DNA. The standard
amplification protocol used in this study consisted of
three distinct steps: DNA denaturation and Taq poly-
merase activation: one cycle at 94°C for one minute;
extension of the two denatured strands: 30 cycles at
94°C for 1min, 50–68°C for 2min and 72 °C for
2min; and termination: one cycle at 72°C for 5min.
Each STS marker was associated with a specific
primer pair and annealing temperature (see supple-
mentary sheet 2). The PCR products were separated
on 2–3% gel agarose, either on a conventional hori-
zontal electrophoresis gel or on an automated capil-
lary electrophoresis gel with fragment analysis tech-
nology (Fragment Analyzer Automated CE System).
SNP genotyping was performed using Kom-
petitive Allele Specific PCR (KASP) assays (LGC
Genomics, LCC, Beverly, MA, USA) according to
established protocols described in Dreisigacker etal.
(2016). Each KASP assay was performed in a total
volume of 10μl, consisting of 5μl of genomic DNA
(46ng), 2.43 μl dd H2O, 2.5 μl 2 × KASP Reaction
Mix, and 0.07 μl Assay Mix. All PCR reagents are
kept on ice before use. The PCR cycle ran as fol-
lows: an initial cycle at 94°C for 15min, followed by
20 cycles at 94°C for 10s, 57°C for 5s and 72°C
for 10s; then 18 cycles at 94°C for 10s, 57°C for
20s and 72°C for 40s (depending on SNP primers)
(see Supplementary Data Sheet 2). The PCR product
obtained was examined by reading fluorescence sig-
nals (PHERAstar FSX, BMG Labtech) at 25°C.
Statistical analyses
The descriptive analysis, including the minimum
value (Min), maximum value (Max), mean value
(M), standard error (SE), standard deviation (SD),
variance (V), coefficient of variation (CV), and fre-
quency distribution of alleles, was calculated using
the Excel software. In order to show the distribution
of accessions according to agronomic characteristics,
Table 1 Durum wheat landraces and advanced cultivars examined in this study
N° Type Country MGB code N° Type Country MGB code N° Type Country MGB code
1 MC Morocco 19 13 LAN Morocco 3123 25 NAC Canada 66035
2 MC Morocco 22 14 LAN Morocco 3149 26 NAC Canada 66040
3 MC Morocco 28 15 LAN Morocco 3152 27 NAC Canada 66064
4 MC Morocco 31 16 LAN Morocco 3210 28 NAC Canada 66067
5 MC Morocco 34 17 LAN Morocco 9358 29 NAC USA 66071
6LAN Morocco 3054 18 LAN Morocco 9404 30 NAC Canada 66076
7LAN Morocco 3083 19 LAN Morocco 9418 31 NAC Canada 66077
8LAN Morocco 3093 20 LAN Morocco 9430 32 NAC USA 66078
9LAN Morocco 3101 21 LAN Morocco 16563 33 NAC USA 66079
10 LAN Morocco 3108 22 LAN Morocco 16655 34 NAC USA 66091
11 LAN Morocco 3117 23 LAN Morocco 16662
12 LAN Morocco 3119 24 NAC Canada 66023
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principal component analysis (PCA) was performed
using the IBM SPSS Statistics program (version 22;
SPSS, Armonk, New York).
Results
Descriptive analysis for the agronomic
characterization of the durum wheat collection
The statistical parameters related to starch content,
grain size and grain weight of all durum wheat acces-
sions are presented in Table 2. The durum wheat
accessions showed significant variation with a CV
for the seven agronomic traits ranging from 3.11% to
13.81%. TKW had the highest CV (13.81%), followed
by A with a CV of 7.84%, and L with a CV of 6.50%.
Other traits with lower CV values were P (5.60%),
SW (4.75%), SC (3.68%), and W (3.11%).
Comparing the means between durum wheat
groups, the North- American cultivars (NAC) showed
the highest values for all seed characteristics except
for the W, which was second to the MC group with a
mean of 2.20mm (Fig.1A). The Moroccan cultivars
(MC) showed a value of 2.22mm for W. Landraces
(LAN) had the lowest mean values for all seed char-
acteristics such as P (15.43mm), L (5.29mm), and
SW (79.66kg/hl).
Principal component analysis (PCA) of seed char-
acteristics showed that the first two principal compo-
nents (PC-1 and PC-2) explained 71% of the varia-
tion (Fig.1B). The accessions were divided into three
groups according to their grain characteristics, with
NAC accessions being most closely clustered around
the attributes, MC accessions intermediate and LAN
accessions furthest away. This is evident in the clus-
ter centroids, with NAC closest to the attributes, MC
intermediate, and LAN in the opposite zone of PC-1.
According to PCA, seed characteristics revealed
significant correlations, specifically between SW and
grain size, as well as among grain dimensions L, W,
A, and P (Fig.1C). The correlation between SW and
all other grain dimensions was significant and nega-
tive. Among the grain dimensions, all correlations
were positive and strong, except for the correlation
between L and W which was not significant. No other
correlations were found to be significant.
Frequency distribution of favorable and unfavorable
alleles
Table3 presents the observed allele frequencies for
the 14 molecular markers used. Only 4 polymor-
phic loci were identified. In contrast, the remain-
ing ten loci were monomorph (Wx-A1, TaCwi-A1,
TaGW2, TGW6-4A, TaSus2-2A, TaSus2-2B, and
TGW6TaSus1-7A-1185, TaSus1-7A-1599, and
TaSus1-7A-3544). The polymorphic loci were Wx-
B1, TaCwi-4A, TaGS5-A1, and TaSus1-7B. At the
Wx-B1 locus, the alleles Wx-B1b and Wx-B1a had
the same frequency. At the TaCwi-4A locus, the
undesirable allele Hap-4A-C was more frequent
than the desirable allele Hap-4A-T. The undesir-
able allele TaGS5-A1a at the TaGS5-A1 locus was
more prominent (85.3%) among accessions, while
the desirable allele TaGS5-A1b was rare (14.7%)
and found only in a few accessions, e.g., MC lines
MGB-22 and MGB-31, LAN MGB-3083 and MGB-
3123, and NAC line MGB-66067. At the TaSus1-
7B locus, 97.05% of accessions had the desirable
Table 2 Descriptive statistics for durum wheat grain sizes for all accessions
SC Starch content, TKW Thousand kernel weight, SW Specific weight, A Area, P Perimeter, L Length, W Width, Min Minimum
value, Max Maximum value, ES Error standard, SD Standard deviation, V Variance, CV Coefficient of variation
Grain sizes Min Max M ± ES SD V CV (%)
SC (mg/g) 68.3 78.31 73.28 ± 0.46 2.69 7.26 3.68
TKW (g) 41 66 50 ± 0.01 0.07 0 13.81
SW (kg/hl) 70 86.2 80.33 ± 0.65 3.81 14.54 4.75
A (mm2) 7.98 10.81 9.1 ± 0.12 0.71 0.51 7.84
P (mm) 14.13 18.01 15.47 ± 0.15 0.87 0.75 5.6
L (mm) 4.72 6.39 5.3 ± 0.06 0.34 0.12 6.5
W (mm) 2.05 2.31 2.19 ± 0.01 0.07 0 3.11
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allele Hap-T, with one NAC carrying the undesir-
able allele Hap-C. For the seven monomorphic loci,
most were fixed for the desirable allele, except for
the TGW6 locus, which was fixed for the undesir-
able allele TaTGW6-A1b. The desirable alleles were
Wx-A1a allele at the Wx-A1 locus, the TaCwi-A1a
allele at the TaCwi-A1 locus, the Hap-6A-A allele
at the TaGW2 locus, the TaTGW6-b allele at the
TGW6-4A locus, the Hap-A allele at the TaSus2-2A
locus, and the Hap-L allele at the TaSus2-2B locus.
The other monomorphic alleles included haplotypes
Hap2, 4 (TaSus1-7A-1185), Hap1, 2, 3 (TaSus1-
7A-1599), and Hap2, 3, 4 (TaSus1-7A-3544).
Comparison of favorable and unfavorable alleles
among groups
Concerning the distribution of favorable and unfa-
vorable alleles between the groups, the LAN LC were
found to contain more accessions carrying favorable
alleles compared to the other two groups. At the Wx-
B1 locus, the Wx-B1b allele was observed in thirteen
LAN, two MC, and two NAC. At the TaCwi-4A locus,
the desirable haplotype Hap-4A-T was present in 5
LAN, 4 NAC, and 3 MC. At the TaGS5-A1 locus, 5
accessions had the desirable allele TaGS5-A1b, while
15 LAN, 10 NAC, and 3 MC carried the undesirable
65 70 75 80
MC
LAN
NAC
All Acc
SC (mg/g)
0510 15
MC
LAN
NAC
All Acc
A (mm²)
13 14 15 16 17
MC
LAN
NAC
All Acc
P (mm)
44.5 55.5 6
MC
LAN
NAC
All Acc
L (mm)
22.1 2.22.3
MC
LAN
NAC
All Acc
W (mm)
70 75 80 85 90
MC
LAN
NAC
All Acc
SW (kg/hl)
44 46 48 50 52 54
MC
LAN
NAC
All Acc
TKW (g)
(A)
PC-2 (18.37%)
(B)
PC-1 (52.20%)
(C)
PC-2 (18.37%)
PC-1 (52.20%)
Fig. 1 Comparison of groups based on grain characteristics.
A Mean values of grain characteristics for all accessions and
groups. B Distribution of accessions by grain characteristics
using Principal Component Analysis (PCA). PCA accounted
for approximately 71% of the total variation, with PC-1 and
PC-2 explaining 52.52% and 18.37% respectively. C Cor-
relation between studied traits according to PCA. All Acc All
accessions, LAN Landraces, MC Moroccan cultivars, NAC
North American cultivars, SC Starch content, TKW Thousand
kernel weight, SW Specific weight, A Area, P Perimeter, L
Length, W Width
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allele TaGS-A1a. For the TaSus1-7B locus, all LAN,
NAC and MC had the desirable haplotype Hap-
T, except for a single NAC accession MGB-66040
which carried the unfavorable haplotype Hap-C
(Fig.2).
Number of favorable alleles per accession
The results of the number of favorable alleles for each
accession are shown in Fig.3. The favorable alleles
in each accession ranged from 9 to 12 with an aver-
age of 10. The accession with the highest number of
favorable alleles, 12, was a single LAN named MGB-
3083. Four accessions, including one MC MGB-22,
one LAN MGB-3101, and two NAC MGB-66035
and MGB-66067, contained 11 favorable alleles.
Accessions with 9 favorable alleles were MC MGB-
28, LAN MGB-3152, NAC MGB-66023, MGB-
66064, MGB-66071, MGB-66076, MGB-66077,
MGB-66079, and MGB-66091.
Discussion
Intensive selection in breeding may lead to a nar-
row genetic base in elite germplasm (Sharma etal.
2021). Therefore, breeding programs have a constant
need to introduce new beneficial genetic diversity, to
enrich the elite germplasm pool with desirable traits
and alleles. Genetic resources of durum wheat such as
landraces and advanced cultivars conserved in Gen-
ebanks are potential sources of such genetic diversity.
Table 3 Molecular markers, alleles, and allelic frequencies for all accessions in the study
Marker type Marker name Alleles Variation Phenotype of alleles Frequency (%)
STS Wx-A1 Wx-A1a wt High starch Desirable allele 100
Wx-A1b Null Low starch Undesirable allele 0
Wx-B1 Wx-B1b Null – – 50
Wx-B1a wt – – 50
SNP TaCwi-A1 TaCwi-A1a A High TKW Desirable allele 100
TaCwi-A1b C Low TKW Undesirable allele 0
TaCwi-4A Hap-4A-T T High TKW Desirable allele 35.29
Hap-4A-C C Low TKW Undesirable allele 64.71
TaGS5-A1 A1b T High TKW Desirable allele 14.7
A1a G Low TKW Undesirable allele 85.3
TaGW2 Hap-6A-A A High TKW Desirable allele 100
Hap-6A-G G Low TKW Undesirable allele 0
TGW6-4A TaTGW6-b C High TKW Desirable allele 100
TaTGW6-a G Low TKW Undesirable allele 0
TaSus1-7A-1185 Hap2, 4, T – – 0
Hap1, 3, 5 C – – 100
TaSus1-7A-1599 Hap4, 5 TT – – 0
Hap1, 2, 3 GA – – 100
TaSus1-7A-3544 Hap2, 3, 4 C – – 100
Hap1, 5 G – – 0
TaSus1-7B Hap-T Ins High TKW Desirable allele 97.05
Hap-C Del Low TKW Undesirable allele 2.95
TaSus2-2A Hap-A A High TKW Desirable allele 100
Hap-G G Low TKW Undesirable allele 0
TaSus2-2B Hap-L T High TKW Desirable allele 100
Hap-H C Low TKW Undesirable allele 0
TGW6 TaTGW6-A1a G High TKW Desirable allele 0
TaTGW6-A1b C Low TKW Undesirable allele 100
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To this end, the present study was conducted to char-
acterize and identify genotypes with good seed char-
acteristics and related alleles that can advance durum
wheat breeding programs. It was of interest to com-
pare seed characteristics of Moroccan (landraces and
cultivars) and North American (Canadian and Ameri-
can) durum wheat, with respect to identify potential
genotypes for increased semolina and flour yield.
Seven traits and 14 loci were investigated.
Our results showed significant genetic variation
among accessions for most traits. Similar results were
found by Zarkti etal. (2010, 2012) and Chegdali etal.
(2020, 2022a, b). Significant variations were shown
for TKW, A, L, and P. The results were comparable to
those of our previous studies (Chegdali etal. 2022a).
The level of genetic variation reflectd the diversity of
the collection examined, involving the type (landraces
and advanced cultivars) and origin (Morocco, Canada
and the USA) of the genotypes considered. This result
may offer possibilities for combining traits to obtain
appropriate characteristics in a specific genotype,
thus meeting the requirements of breeders responsible
for yield improvement.
SC is one of the most widely used biochemi-
cal parameters for the discrimination and classifica-
tion of genotypes. It is the major reserve component
of the kernel contributing to early germination and
seedling growth (Shaik etal. 2014) and an indicator
of semolina milling yield and pasta quality (Joubert
etal. 2016). Furthermore, it is closely associated with
the kernel weight of durum wheat seeds. The lev-
els of SC found in the present study were compara-
ble to those reported by some authors (BeMiller and
Wx-B1a ( -)
Wx-B1b (-)
TaGS5-A1a
(
Unf
)
TaGS5-A1b
(
Fav
)
Hap-C
(
Unf
)
Hap-T
(
Fav
)
Hap-4A-T
(
Fav
)
Hap-4A-C (Unf)
Wx-B1TaCwi-4A
TaGS5-A1 Ta Sus1-7B
NAC
MC
LAN
NAC
MC
LAN
NAC
MC
LAN
NAC
MC
LAN
Fig. 2 The number of favorable and unfavorable alleles of pol-
ymorphic markers for each group. Favorable (Fav) and unfa-
vorable (Unf) alleles are shown in dark gray and blue, respec-
tively. All Acc All accessions, LAN Landraces, MC Moroccan
cultivars, NAC North American cultivars
1
2
3
4
5
6
7
8
9
10
11
12
MGB-19
MGB-22
MGB-28
MGB-31
MGB-34
MGB-3054
MGB-3083
MGB-3093
MGB-3101
MGB-3108
MGB-3117
MGB-3119
MGB-3123
MGB-3149
MGB-3152
MGB-3210
MGB-9358
MGB-9404
MGB-9418
MGB-9430
MGB-16563
MGB-16655
MGB-16662
MGB-66023
MGB-66035
MGB-66040
MGB-66064
MGB-66067
MGB-66071
MGB-66076
MGB-66077
MGB-66078
MGB-66079
MGB-66091
Number of the favorable alleles
Fig. 3 Distribution of the favorable allele number for each
accession
Euphytica (2024) 220:2
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Whistler 2009; Boukid etal. 2018; Chegdali et al.
2022a; Saini etal. 2022). Comparing the mean val-
ues of the groups, the advanced cultivars NAC and
MC had higher values compared to LAN. This was
in agreement with results reported by Boukid et al.
(2018) and Chegdali etal. (2022a) for durum wheat
collections including landraces and modern cultivars
from Tunisia and Morocco, respectively. This implies
that there is a directed selection of high-yielding and
high-starching cultivars. Accessions with higher val-
ues were NAC MGB-66067, MGB-66077, MGB-
66035, MGB-66040, MC MGB-28 and MGB-31, and
LAN accessions MGB-16563, MGB-3123, MGB-
16662, and MGB-9358.
Grain weight and size are major physical char-
acteristics that determine the final milling yield and
quality of a germplasm. Therefore, they are key char-
acteristics used in quality selection during the early
stages of wheat breeding programs (Assadzadeh etal.
2022). In a gene pool rich in valuable traits, TKW,
SW, and grain dimensions are often used to predict
milling yield and identify the best genotypes with
high weight and size for introduction into durum
wheat breeding programs. The results of grain param-
eters for all accessions were similar to those of pre-
vious studies (Troccoli and di Fonzo 1999; Novaro
etal. 2001; Martín-Gómez et al. 2019; Alemu et al.
2020; Chegdali etal. 2022a) for durum wheat geno-
types from Ethiopia, Spain, Italy, and Poland. NAC
showed the highest values for grain weight and size
among the accessions studied, followed by MC, while
LAN accessions show on avearge less favorable seed
characteristics. This finding is consistent with several
previous studies (Abu-Zaitoun et al. 2018; Deside-
rio et al. 2019; Frankin et al. 2021; Chegdali et al.
2022a) which found that grains from old genotypes
have lower weights and smaller sizes compared to
grains from improved genotypes. Desiderio et al.
(2019) reported that improved genotypes often have
an advantage over landraces in terms of uniformity of
kernels with large size and high weight. In contrast,
Moore (2015) found that landraces can also show
high variability in shape and weight. For the rank-
ing of genotypes with the best characteristics in the
current study, the top six genotypes for seed charac-
teristics area (A), perimeter (P), and length (L) were
LAN accessions MGB-9430, MGB-3152, MGB-
66023, MGB-9418, MGB-16563, NAC MGB-66023
and MGB-66040, while for TKW and SW the top
genotypes were NAC MGB-66077, MGB-66078,
MGB-66064, and MGB-66079 and LAN accessions
MGB-16655 and MGB-9404. On the other hand,
LAN accessions MGB-3119, MGB-3123, MGB-
3093, NAC MGB-66023 and MGB-66077, and MC
MGB-19 were among the top six accessions for size
W. These genotypes may have potential to contribute
new beneficial trait variation for grain shape and size
characteristics to the existing elite gene pool and to
improve durum wheat yield and semolina content.
Several previous studies that have shown that small-
sized grains have lower milling yield and lower pasta
quality, while large-sized grains have higher flour
and semolina yield (Troccoli and di Fonzo 1999;
Baasandorj et al. 2015; Wang and Fu 2020; Ficco
et al. 2020). This is due to the high percentage of
endosperm compared to bran and aleurone, as noted
by Ficco etal. (2020).
Strong correlation between grain morphometric
parameters and SW was observed in our study, which
suggests that genotypes with high-yielding flour and
semolina can be selected based by these parameters.
This is supported by the significant indirect correla-
tion found between SW and grain size. Addition-
ally, this study suggests that the prediction of semo-
lina yield may depend on these grain morphometric
parameters and SW, as SW is often strongly corre-
lated with milling productivity. This conclusion is
consistent with the findings of Novaro etal. (2001),
who used image analysis techniques to study durum
wheat and found similar results.
Our study also aimed to identify favorable alleles
linked to grain weight within all accessions and
groups, as well as in each individual accession. We
used molecular markers to assess genetic variation
at 14 loci. Only four of the loci (Wx-B1, TaCwi-4A,
TaGS5-A1, and TaSus1-7B) were found to be poly-
morphic, i.e. each of these loci possesses two distinct
allele types within the collection. The remaining ten
loci (Wx-A1, TaCwi-A1, TaGW2, TGW6-4A, TaSus1-
7A-1185, TaSus1-7A-1599, TaSus1-7A-3544, TaSus2-
2A, TaSus2-2B, and TGW6) were monomorphic, indi-
cating that each of these loci exhibits dominance of a
single allele.
We summarized the frequency of desirable alleles
at all marker loci within each germplasm group. The
highest frequencies of desirable alleles were found in
the LAN group, followed by MC and NAC. This sug-
gests, that although grain weight measures of LAN
Euphytica (2024) 220:2
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were lower than in cultivars, LAN carry valuable
alleles that can be used for introgression in breed-
ing (Chegdali et al. 2020). The sum of marker loci
might not reflect the true, total grain weight value and
explain only a smaller proportion of the trait. Other
research has also shown that landraces are a valuable
source of untapped alleles for wheat breeding and
crop improvement (Rasheed etal. 2016; Zhao et al.
2019; Marone etal. 2021; Taranto etal. 2022). In par-
ticular, LAN had a higher number of desirable alleles
such as Wx-B1b, Hap-4A-T, TaGS5-A1b, and Hap-T
at the Wx-B1, TaCwi-4A, TaGS5-A1, and TaSus1-
7B loci, respectively. The Wx-B1b allele located at
the Wx-B1 locus is a type of null allele for granule-
bound starch synthase (GBSS). The specific impact
of this null allele on different end-use products of
durum wheat is not yet fully understood. Neverthe-
less, some studies have shown that this null allele
is related to waxy proteins and low amylose con-
tent, as well as to the good quality of specific prod-
ucts (Nakamura etal. 1992; Yamamori etal. 1992;
Sharma etal. 2002; Zhang etal. 2008, 2021; Rasheed
etal. 2016; Guzmán and Alvarez 2016; Zhao et al.
2019; Chunduri et al. 2021; Wu et al. 2023). Typi-
cally, this non-functional allele is rare in old durum
wheat (Guzmán etal. 2011), however, in this study
it was found at higher frequency in LAN compared
to the advanced cultivars. However, in our previous
study (Chegdali etal. 2022a, b) and other studies such
as Rasheed etal. (2016) and Zhao etal. (2019), this
allele was present in fewer numbers in landraces and
moderate to high numbers in advanced cultivars. In
general, reduced amylose content in wheat genotypes
is preferable for the end-use quality of certain wheat
products, such as noodles, bread, and pasta (Naka-
mura etal. 1992; Yamamori etal. 1992; Sharma etal.
2002; Baik etal. 2003; Chunduri etal. 2021; Zhang
etal. 2021; Li etal. 2022; Wu etal. 2023). Therefore,
its presence in LAN could be considered an advan-
tage for improving local wheat breeding. Concerning
the TaCwi-A4 marker, this locus controls a cell wall
conversion enzyme that hydrolyzes sugar into glucose
and fructose and has recently been found to be cor-
related with wheat yield (Jiang etal. 2015; Rasheed
etal. 2016; Sehgal etal. 2019). This locus is particu-
larly associated with seed weight and has two hap-
lotypes, Hap-4A-T and Hap-4A-C, which are alleles
linked to high and low TKW, respectively (Ma etal.
2012; Jiang et al. 2015). In this study, as with the
Wx-B1 locus, LAN ranked first in terms of the num-
ber of accessions carrying the favorable Hap-4A-T
allele at the TaCwi-4A locus, followed by NAC and
then MC. This distribution was not consistent with
our previous study (Chegdali etal. 2022a) where we
found that this favorable allele was not prevalent in
landraces. Researchers have reported that the Hap-
4A-T allele is generally dominant in breeding lines
and is highly valued by breeders because of its asso-
ciation with high TKW (Jiang et al. 2015; Rasheed
et al. 2016). Therefore, increasing the frequency of
this haplotype in new varieties could be useful for
improving local yield productivity. The TaGS5-A1
gene is also commonly used for seed traits. It has
been identified as having two alleles named TaGS5-
A1a and TaGS5-A1b, and the TaGS5-A1b allele has
been found to be associated with relatively larger
grain width and higher TKW (Wang et al. 2015;
Ma et al. 2016; Sehgal et al. 2019). This favorable
allele is present in only four accessions: two LAN
(MGB-3083 and MGB-3123), one MC (MGB-22
and MGB-31) and one NAC (MGB-66067). Li etal.
(2019) also found a significant predominance of the
unfavorable allele TaGS5-A1a over the favorable
allele TaGS5-A1b in a collection of winter wheat
cultivars and breeding lines. The distribution of this
allele in the present study is similar to that found in
the study of Wang etal. (2015), in which the favora-
ble TaGS5-A1b allele was more common in landraces
than in advanced cultivars. For the last polymorphic
locus, TaSus1-7B, all accessions in the collection
carried the desirable haplotype Hap-T, except for a
single accession, NAC MGB-66040, which carried
the unfavorable haplotype Hap-C. The prevalence of
this haplotype was similar to that found in our previ-
ous study (Chegdali etal. 2022a) for a collection of
64 durum wheat accessions and to that found by Hou
et al. (2014) for a collection of 1,520 wheat acces-
sions, including tetraploids, landraces, and modern
cultivars. Therefore, the accumulation of this allele in
current genotypes would likely accelerate and stead-
ily increase yield potential by introducing it to geneti-
cally improve critical yield-related traits, particularly
TKW. This favorable haplotype is known to have a
strong association with high TKW, derived from the
TaSus1-7B locus, which controls the catalytic activity
of sucrose synthase, the first step in the conversion of
sucrose to starch (Jiang etal. 2011; Hou etal. 2014).
Euphytica (2024) 220:2
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For t seven monomorphic loci accessions showed
complete dominance of favorable alleles for six loci,
except for the TGW6 locus where all accessions car-
ried the unfavorable allele named TaTGW6-A1b. For
example, we observed total dominance of the allele
Wx-A1a at the Wx-A1 locus, the allele TaCwi-A1a at
the TaCwi-A1 locus, the haplotype Hap-6A-A at the
TaGW2 locus, the allele TaTGW6-b at the TGW6
locus, the allele Hap-A at the TGW6-4A locus, the
allele TaSus2-2A at the TaSus2-2A locus, and the hap-
lotype Hap-L at the TaSus2-2B locus. These results
were similar to our previous study (Chegdali etal.
2022a). Our outstanding results for the TGW6 locus
were similar to those of our previous study (Cheg-
dali etal. 2022a), but differ from those of Hanif etal.
(2015), Li et al. (2019), Sehgal et al. (2019), and
Cristina etal. (2022). These previous studies found a
high proportion of the favorable TaTGW6-A1a allele
(associated with higher TKW) and a low proportion
of the undesirable TaTGW6-A1b allele in soft wheat
accessions. They also reported that the TaTGW6-
A1a allele was positively selected in wheat breeding.
However, our study did not observe this, suggesting
that the introduction of this allele into new cultivars
should be considered.
Identifying the number of favorable alleles per
accession can be a useful tool in selection. Even if
these markers have little impact on individual traits,
a high number of favorable alleles linked to multiple
grain parameters in a given accession can make it eas-
ier to combine superior alleles from a donor parent,
allowing for the rapid creation of new cultivars with
improved yields (Liu etal. 2022). Our study found
that the number of favorable alleles in each accession
was significant compared to study of Li etal. (2020).
This suggested that the integration of favorable alleles
related to grain characteristics can improve wheat
yield. Additionally, we identified five accessions that
carried more than 11 favorable alleles: MC MGB-22,
LAN MGB-3101, and two NAC MGB-66035 and
MGB-6606, as well as LAN MGB-3083 with up to
12 favorable alleles. These accessions can be consid-
ered as potential parents for wheat breeding.
Conclusion
In conclusion, this study aimed to identify the acces-
sions with desirable traits and alleles in a collection
of durum wheat in order to improve productivity. The
results showed significant genetic variation as well
as significant differences in agronomic and morpho-
metric characteristics among accessions. The exami-
nation of 14 loci revealed four polymorphic and ten
monomorphic loci and found that landraces contain
valuable alleles that might contribute to durum wheat
breeding in Morocco. Favorable genotypes and alleles
may be utilized in future breeding programs to poten-
tially enhance durum wheat productivity in Morocco.
Acknowledgements The authors express gratitude for the
financial support from the CRP-Wheat program of the CGIAR
consortium, University of Hassan 1st Settat (Morocco),
ICARDA/Morocco program for conservation of plant genetic
resources (MCGP), and Global Wheat Program—International
Maize and Wheat Improvement Center (CIMMYT). Carlos
Guzman also acknowledges funding from the European Social
Fund and Spanish State Research Agency (Ministry of Science,
Innovation and Universities) through the Ramon y Cajal Pro-
gram (RYC-2017-21891).
Author contributions YC conducted the investigation and
wrote the original draft, while all authors contributed equally to
resources, conceptualization, writing, editing and proofreading.
All authors reviewed and approved the final manuscript.
Funding Financial support was provided by CRP-Wheat,
University of Hassan 1st Settat, ICARDA/Morocco program,
Global Wheat Program, European Social Fund and Spanish
State Research Agency (Ministry of Science, Innovation).
Data availability Data is provided in the manuscript and
electronic supplementary material.
Declarations
Conflict of interest No personal, professional, or financial
conflicts of interest exist for this study.
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