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Table 10.1.
Examples of the number of SNP markers that are polymorphic between two parental lines of potential
combinations for intra- (e.g., IITA x IITA) and inter- (e.g., IITA x INERA) breeding program crosses.
Parent 1
Parent 2
Cross Type
No. Polymorphic markers
IT84S-2246
IT93K-503-1
IITA x IITA
134
IT89KD-288
Suvita-2
IITA x INERA
245
KVx 525
KVx 396-4-5-20
INERA x INERA
257
KVx 442-3
KVx 396-4-5-20
INERA x INERA
261
Suvita-2
Melakh
INERA x ISRA
274
IT97K-499-35
Mouride
IITA x ISRA
289
Suvita-2
Calif. Blackeye No. 27
INERA x UCR
291
IT84S-2246
IT00K-1263
IITA x IITA
294
IT97K-499-35
IT00K-1263
IITA x IITA
309
KVx 525
Bambey 21
INERA x ISRA
313
Bambey 21
Melakh
ISRA x ISRA
325
IT84S-2246
IT82E-18
IITA x IITA
329
KVx61-1
Calif. Blackeye No. 50
INERA x UCR
339
Melakh
Calif. Blackeye No. 27
ISRA x UCR
343
Yacine
Calif. Blackeye No. 50
ISRA x UCR
345
IT84S-2246
Mouride
IITA x ISRA
347
IT89KD-288
Calif. Blackeye No. 50
IITA x UC R
372
IT93K-503-1
Bambey 21
IITA x ISRA
376
IT82E-18
KVx 525
IITA x INERA
381
IT93K-503-1
Calif. Blackeye No. 27
IITA x UCR
391
needed for marker-assisted breeding. The use-
fulness of a genetic linkage map to plant breed-
ers is determined largely by its thoroughness of
genome coverage, with markers that are highly
polymorphic in target breeding germplasm.
The first version of the cowpea consensus
genetic linkage map was the product of merging
individual genetic maps built from 6 recombi-
nant inbred line (RIL) populations that had been
genotyped with the 1,536 Illumina GoldenGate
Assay (Muchero et al. 2009). This map included
928 markers spanning 11 linkage groups over a
total map distance of 680 centiMorgans (cM).
Map refinement has continued since then, with
the genotyping of five additional RILs and two
F
4
breeding populations, construction of indi-
vidual maps for these populations, and inte-
gration of these maps into an improved con-
sensus map (Figure 10.1) (Lucas et al. 2011).
These new map inputs resulted in improved
marker order and density and fewer gaps, with
the addition of 179 SNP markers (bringing
total markers to 1,107) with an average dis-
tance between markers of about 0.6 cM. Further
HighQuality Consensus
Genetic Map
Breeders have often conducted their marker
breeding programs based on map information
derived from a single cross. Two major limita-
tions of using a single-cross map for the analysis
of marker or gene segregation in a population
are (1) the limited number of traits of economic
importance that will segregate in any one popu-
lation and (2) the limited number of polymorphic
markers. Hence, a second key resource needed
for modern cowpea breeding is a high qual-
ity consensus genetic map. Consensus maps are
formed from merging multiple individual link-
age maps. By the term 'high quality' we mean
marker positions determined with precision and
of sufficient density across the genome. Merg-
ing markers from several populations increases
marker density and the precision of marker posi-
tion estimation, as well as the quantity of mapped
traits. Consensus genetic linkage maps provide
breeders with a resource for analyzing the inher-
itance of traits and marker-trait associations
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