ICRISAT Archival Report 2006 - The seedlings of success in the ...
ICRISAT Archival Report 2006 - The seedlings of success in the ...
ICRISAT Archival Report 2006 - The seedlings of success in the ...
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(Fig. 3), which maybe attributed to <strong>the</strong> geographic orig<strong>in</strong> <strong>of</strong> <strong>the</strong>se accessions. This is also confirmed when<br />
PCoA was performed consider<strong>in</strong>g botanical varieties (Fig. 3). <strong>The</strong> wild accessions formed a different cluster <strong>in</strong><br />
both <strong>the</strong> cases and grouped with hypogaea types, <strong>in</strong>dicat<strong>in</strong>g a close relation between <strong>the</strong>m (Fig. 3 & 4).<br />
Factorial analysis: Axes 1 / 2<br />
vulgaris<br />
vulgaris vulgaris<br />
.3<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris vulgaris vulgaris<br />
vulgaris vulgaris vulgaris<br />
vulgaris vulgaris<br />
vulgaris<br />
vulgaris vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris vulgaris<br />
vulgaris vulgaris vulgaris<br />
vulgaris vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
peruviana<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
hypogaea hypogaea<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris vulgaris<br />
vulgaris<br />
vulgaris vulgaris hypogaea<br />
.2 vulgarishypogaea<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris vulgaris<br />
hypogaea vulgaris<br />
hypogaea<br />
vulgaris<br />
aequatoriana<br />
vulgaris<br />
vulgaris vulgaris vulgaris<br />
vulgaris hypogaea<br />
vulgaris<br />
vulgaris<br />
hypogaea hypogaea vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris vulgaris vulgaris<br />
vulgaris vulgaris<br />
vulgaris vulgaris<br />
Wild<br />
hypogaea<br />
vulgarishypogaea<br />
vulgaris<br />
hypogaea<br />
vulgaris<br />
hypogaea<br />
vulgaris<br />
fastigiata<br />
vulgaris<br />
fastigiata<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
fastigiata<br />
vulgaris<br />
vulgaris vulgaris<br />
hypogaea<br />
vulgaris<br />
fastigiata<br />
vulgaris hypogaea vulgaris<br />
hypogaea<br />
hypogaea hypogaea<br />
hypogaea<br />
vulgaris<br />
vulgaris<br />
hypogaea hypogaea<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
hypogaea hypogaea<br />
vulgaris vulgaris<br />
vulgaris<br />
hypogaea hypogaea<br />
hypogaea<br />
vulgaris<br />
hypogaea<br />
fastigiata<br />
vulgaris<br />
vulgaris vulgaris vulgaris<br />
vulgaris<br />
vulgaris vulgaris<br />
vulgaris<br />
vulgaris<br />
hypogaea vulgaris<br />
vulgaris vulgaris hypogaea hypogaea<br />
vulgaris<br />
vulgaris<br />
hypogaea<br />
hypogaea<br />
hypogaea<br />
vulgaris<br />
fastigiata<br />
vulgaris<br />
.1<br />
peruviana<br />
hypogaea<br />
vulgaris vulgaris<br />
vulgaris<br />
hypogaea<br />
vulgaris vulgaris<br />
hypogaea vulgaris<br />
hypogaea<br />
vulgaris<br />
vulgaris vulgaris<br />
vulgaris<br />
hypogaea<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
hypogaea fastigiata vulgaris<br />
vulgaris<br />
hypogaea hypogaea hypogaea hypogaea<br />
vulgaris<br />
vulgaris<br />
fastigiata vulgaris vulgaris<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
hypogaea<br />
vulgaris<br />
hypogaea vulgaris<br />
hypogaea<br />
hypogaea<br />
vulgaris hypogaea vulgaris vulgaris<br />
hypogaea<br />
hypogaea<br />
hypogaea<br />
vulgaris<br />
vulgaris vulgaris<br />
hypogaea<br />
vulgaris vulgaris<br />
hypogaea<br />
Wild<br />
fastigiata<br />
vulgaris<br />
hypogaea fastigiata<br />
vulgaris<br />
vulgaris peruviana vulgaris<br />
vulgaris<br />
hypogaea<br />
hypogaea<br />
vulgaris<br />
vulgaris<br />
hypogaea hypogaea hypogaea vulgaris<br />
vulgaris<br />
hypogaea vulgaris<br />
hypogaea<br />
hypogaea<br />
hypogaea<br />
hypogaea hypogaea<br />
hypogaea<br />
hypogaea<br />
vulgaris<br />
fastigiata<br />
Wild hypogaea<br />
vulgaris vulgaris vulgaris<br />
hypogaea<br />
fastigiata hypogaea<br />
peruviana<br />
aequatoriana vulgaris<br />
hypogaea<br />
peruviana<br />
vulgaris<br />
hypogaea<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
peruviana<br />
vulgaris peruviana<br />
fastigiata<br />
vulgaris peruviana vulgaris hypogaea<br />
hypogaea hypogaea<br />
hypogaea<br />
hirsuta<br />
hypogaea<br />
hypogaea<br />
hypogaea<br />
hypogae<br />
vulgaris<br />
vulgaris vulgaris vulgaris<br />
hypogaea<br />
hypogaea<br />
hypogaea<br />
hypogaea<br />
vulgaris<br />
hypogaea<br />
vulgaris<br />
vulgaris<br />
hypogaea<br />
hypogaea<br />
vulgaris vulgaris<br />
peruviana peruviana peruviana<br />
hypogaea<br />
hypogaea hypogaea<br />
hypogaea<br />
hypogaea<br />
vulgaris<br />
vulgaris<br />
hypogaea Wild vulgaris hypogaea<br />
hypogaea hypogaea<br />
fastigiata<br />
hypogaea<br />
hypogaea<br />
fastigiata<br />
peruviana<br />
peruviana aequatoriana<br />
vulgaris<br />
hypogae<br />
hypoga<br />
hypogaea<br />
vulgaris hypogaea<br />
hypogaea<br />
vulgaris<br />
hypogaea Wild<br />
hypogaea<br />
hypogaea vulgaris<br />
vulgaris<br />
hypogaea<br />
hypogaea<br />
hypogaea<br />
hypogaea<br />
Wild vulgaris<br />
vulgaris<br />
hypogaea<br />
hypogaea<br />
hypogaea<br />
hypogaea<br />
hypogaea vulgaris hypogaea vulgaris<br />
Wild Wildvulgaris<br />
vulgaris<br />
hypogaea<br />
hypogaea<br />
hypogaea<br />
vulgaris<br />
Wild<br />
vulgaris hypogaea<br />
hypogaea hypogaea hypogaea<br />
-.5 -.4 -.3 -.2 -.1 .1<br />
peruviana<br />
.2<br />
hypogaea<br />
fastigiata<br />
.3 vulgaris vulgaris<br />
.4<br />
vulgaris<br />
peruviana vulgaris<br />
hypogaea<br />
vulgaris<br />
vulgaris<br />
hypogaea<br />
hypogaea<br />
hypogaea hypogaeahypogaea<br />
vulgaris<br />
fastigiata fastigiata<br />
fastigiata<br />
hypogaea<br />
Wild<br />
hypogaea<br />
hypogaea vulgaris<br />
peruviana<br />
fastigiata fastigiata<br />
peruviana<br />
fastigiata<br />
hypogaea<br />
hypogaea<br />
hypogaea<br />
hypogaea peruviana<br />
hypogaea<br />
peruviana fastigiata<br />
hypogaea<br />
hypogaea vulgaris vulgaris<br />
Wild vulgaris<br />
hypogaea<br />
vulgaris<br />
hypogaea<br />
hypogaea<br />
vulgaris<br />
Wild<br />
vulgaris<br />
peruviana<br />
fastigiata<br />
hypogaea hypogaea<br />
hypogaea hypogaea<br />
Wild<br />
vulgaris<br />
hypogaea<br />
vulgaris<br />
peruviana fastigiata<br />
peruviana<br />
hypogaea<br />
hypogaea hypogaea hypogaea<br />
hypogaea<br />
vulgaris<br />
vulgaris Wild<br />
vulgaris<br />
vulgaris fastigiata<br />
Wild Wild<br />
hypogaea<br />
hypogaea<br />
fastigiata<br />
vulgaris<br />
hypogaea<br />
fastigiata<br />
hypogaea<br />
hypogaea<br />
vulgaris<br />
Wild Wild Wild Wild<br />
fastigiata<br />
vulgaris<br />
peruviana fastigiata<br />
peruviana hypogaea<br />
hypogaea hypogaea<br />
hypogaea hypogaea<br />
vulgaris<br />
-.1<br />
fastigiata<br />
peruviana<br />
hypogaea<br />
vulgaris<br />
vulgaris<br />
hypogaea<br />
vulgaris<br />
vulgaris<br />
vulgaris<br />
hypogaea<br />
fastigiata vulgaris<br />
Wild Wild<br />
Wild<br />
Wild<br />
Wild Wild<br />
Wild<br />
Wild<br />
Wild<br />
fastigiata<br />
Wild Wild<br />
vulgaris<br />
Wild<br />
Wild hypogaea hypogaea<br />
fastigiata<br />
fastigiata<br />
fastigiata vulgaris<br />
Wild<br />
fastigiata<br />
Wild Wild Wild Wild<br />
Wild fastigiata<br />
Wild<br />
vulgaris<br />
vulgaris<br />
hirsuta<br />
fastigiata<br />
Wild<br />
vulgaris<br />
-.2<br />
fastigiata vulgaris fastigiata<br />
fastigiata<br />
vulgaris fastigiata fastigiata<br />
fastigiata<br />
fastigiata<br />
Wild<br />
vulgaris<br />
vulgaris<br />
fastigiata<br />
vulgaris<br />
fastigiata vulgaris<br />
vulgaris fastigiata<br />
vulgaris<br />
fastigiata fastigiata<br />
vulgaris fastigiata<br />
fastigiata<br />
hypogaea<br />
vulgaris fastigiata<br />
-.3<br />
fastigiata<br />
fastigiata vulgaris fastigiata<br />
fastigiata<br />
vulgaris vulgaris<br />
fastigiata fastigiata<br />
fastigiata fastigiata fastigiata vulgaris<br />
vulgaris fastigiata<br />
fastigiata<br />
fastigiata<br />
fastigiata<br />
fastigiata<br />
-.4<br />
fastigiata<br />
fastigiata fastigiata<br />
fastigiata<br />
fastigiata<br />
fastigiata<br />
fastigiata<br />
fastigiata<br />
fastigiata fastigiata<br />
fastigiata fastigiata fastigiata fastigiata<br />
fastigiata fastigiata fastigiata<br />
fastigiata fastigiata fastigiata<br />
fastigiata<br />
fastigiata<br />
fastigiata<br />
fastigiata<br />
fastigiata fastigiata<br />
fastigiata<br />
-.5<br />
fastigiata<br />
fastigiata<br />
fastigiata fastigiata fastigiata<br />
fastigiata<br />
fastigiata<br />
fastigiata<br />
fastigiata<br />
fastigiata<br />
fastigiata fastigiata<br />
fastigiata<br />
fastigiata<br />
fastigiata fastigiata<br />
fastigiata<br />
fastigiata<br />
-.6<br />
fastigiata: Red; hypogaea: Black; peruviana: Blue; vulgaris: Orange; hirsuta: P<strong>in</strong>k; aequatoriana: Magenta;<br />
Wild: Light green<br />
Fig. 4. Factorial analysis at <strong>the</strong> level <strong>of</strong> botanical varieties.<br />
Fur<strong>the</strong>r analysis <strong>of</strong> data is <strong>in</strong> progress to fully understand <strong>the</strong> genetic structure <strong>of</strong> groundnut composite<br />
collection. <strong>The</strong> results from genotypic data will be used to select <strong>the</strong> reference set <strong>of</strong> 300 accessions for future<br />
use.<br />
To ascerta<strong>in</strong> <strong>the</strong> quality and position <strong>of</strong> <strong>the</strong> SSR markers, <strong>the</strong>se will be checked on 15-20 plants <strong>in</strong> each <strong>of</strong> three<br />
F 2 populations, whose parents have been <strong>in</strong>cluded <strong>in</strong> <strong>the</strong> composite collection. Only those SSR markers that<br />
showed polymorphism on <strong>the</strong> parents will be checked on <strong>the</strong> F 2 population. Three crosses <strong>in</strong>volv<strong>in</strong>g five parents<br />
have been selected for this purpose and 14 out <strong>of</strong> 21 markers have been found to be polymorphic between <strong>the</strong><br />
parental comb<strong>in</strong>ations. <strong>The</strong> F 2 populations are be<strong>in</strong>g genotyped presently and <strong>the</strong> results will confirm <strong>the</strong><br />
location/position <strong>of</strong> <strong>the</strong>se SSR markers and would ensure appropriate peak call<strong>in</strong>g. Data generated from <strong>the</strong><br />
f<strong>in</strong>gerpr<strong>in</strong>t<strong>in</strong>g will be <strong>the</strong>n subjected to statistical analysis us<strong>in</strong>g different computational tools.<br />
HD Upadhyaya, R Bhattacharjee, CLL Gowda,<br />
RK Varshney and DA Hois<strong>in</strong>gton.<br />
Milestone C.3.1.15: Diversity and population structure <strong>of</strong> pigeonpea composite collection analyzed and<br />
reference set (300 accessions) established (HDU/RB/RKV/DH/SC/JB, 2009)<br />
At <strong>ICRISAT</strong>, genotyp<strong>in</strong>g <strong>of</strong> 1000 accessions (composite collection) was carried out. DNA was extracted from<br />
12 plants per accession and a series <strong>of</strong> artificial pools hav<strong>in</strong>g different proportions <strong>of</strong> two genotypes show<strong>in</strong>g<br />
polymorphism for a given SSR marker were developed and screened with <strong>the</strong> correspond<strong>in</strong>g polymorphic SSR<br />
marker. <strong>The</strong> coefficients <strong>of</strong> correlations were analyzed between different proportion <strong>of</strong> alleles recorded<br />
(correspond<strong>in</strong>g to 12 plants per accession) and proportion <strong>of</strong> genomic DNA used for <strong>the</strong> correspond<strong>in</strong>g<br />
accession. As a result, 20 SSR markers with highly significant correlations (r 2 > 0.9) were identified.<br />
<strong>The</strong> selected 20 polymorphic SSR markers were optimized for PCR reactions follow<strong>in</strong>g Taguchi method<br />
(Taguchi, 1986) as described <strong>in</strong> Cobb and Clarkson (1994). A fluorescent-based multiplex genotyp<strong>in</strong>g system<br />
was <strong>the</strong>n used to generate different multiplexes, which were used to f<strong>in</strong>gerpr<strong>in</strong>t <strong>the</strong> composite collection. <strong>The</strong><br />
amplified PCR products were separated by capillary electrophoresis <strong>in</strong> an automated system us<strong>in</strong>g ABI 3700.<br />
SSR fragment sizes were called to two decimal places us<strong>in</strong>g <strong>the</strong> Genotyper v 3.7 s<strong>of</strong>tware. <strong>The</strong> allelic data was<br />
analyzed follow<strong>in</strong>g allele b<strong>in</strong>n<strong>in</strong>g algorithm, written <strong>in</strong> a C program at <strong>ICRISAT</strong> called as “Allelob<strong>in</strong>”, based on<br />
<strong>the</strong> least squares algorithm <strong>of</strong> Idury and Cardon (1997). Less than 5% miss<strong>in</strong>g data (i.e. marker x genotype) was<br />
recorded <strong>in</strong> <strong>the</strong> dataset and all <strong>the</strong> markers produced allele size that was expected on <strong>the</strong> basis <strong>of</strong> repeat motif <strong>of</strong><br />
each <strong>of</strong> <strong>the</strong> SSR markers. Prelim<strong>in</strong>ary analysis has been completed on 17 out <strong>of</strong> 20 markers and 3 markers<br />
showed poor quality <strong>in</strong>dex (Table 6), which may be due to high miss<strong>in</strong>g vales recorded for <strong>the</strong>se markers.<br />
Prelim<strong>in</strong>ary analysis detected a total <strong>of</strong> 184 alleles, rang<strong>in</strong>g from 2 (PKS18) to 24 (CCB8) with a mean <strong>of</strong> 10.8<br />
alleles per locus and mean PIC value <strong>of</strong> 0.31 (rang<strong>in</strong>g from 0.02 to 0.0.59) (Table 7).<br />
64
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