A panel of 60 genotypes comprising New Plant Types (NPTs) along with
indica
,
tropical
and
temperate japonica
genotypes was phenotypically evaluated for four seasons in irrigated situation for grain yield
per se
and component traits. Twenty NPT genotypes were found promising with an average grain yield varying from 5.45 to 8.8 t/ha. A total of 85 SSR markers were used in the study to identify QTLs associated with grain yield
per se
and related traits. Sixty-six (77.65%) markers were found to be polymorphic. The PIC values varied from 0.516 to 0.92 with an average of 0.704. A moderate level of genetic diversity (0.39) was detected among genotypes. Variation to the tune of 8% within genotypes, 68% among the genotypes within the population and 24% among the populations were observed (AMOVA). This information may help in identification of potential parents for development of transgressive segregants with very high yield. The association analysis using GLM and MLM models led to the identification of 30 and 10 SSR markers associated with 70 and 16 QTLs, respectively. Thirty novel QTLs linked with 16 SSRs were identified to be associated with eleven traits, namely tiller number (
qTL-6
.
1
,
qTL-11
.
1
,
qTL-4
.
1
), panicle length (
qPL-1
.
1
,
qPL-5
.
1
,
qPL-7
.
1
,
qPL-8
.
1
), flag leaf length (
qFLL-8
.
1
,
qFLL-9
.
1
), flag leaf width (
qFLW-6
.
2
,
qFLW-5
.
1
,
qFLW-8
.
1
,
qFLW-7
.
1
), total no. of grains (
qTG-2
.
2
,
qTG-a7
.
1
), thousand-grain weight (
qTGW-a1
.
1
,
qTGW-a9
.
2
,
qTGW-5
.
1
,
qTGW-8
.
1
), fertile grains (
qFG-7
.
1
), seed length-breadth ratio (
qSlb-3
.
1
), plant height (
qPHT-6
.
1
,
qPHT-9
.
1)
, days to 50% flowering (
qFD-1
.
1
) and grain yield per se (
qYLD-5
.
1
,
qYLD-6
.
1a
,
...
