use Modern::Perl;
use Data::Dumper;

my %HoAoArrays;

while (<DATA>) {
    chomp;
    my ( $col0, @cols1_3 ) = split /\t/;
    push @{ $HoAoArrays{$col0} }, \@cols1_3;
}

for my $key ( keys %HoAoArrays ) {
    my $numElements= @{ $HoAoArrays{$key} };
    
    for ( my $i = 0 ; $i < $numElements; $i++ ) {
        say '${ $HoAoArrays{' 
          . $key . '} }[' 
          . $i
          . ']->[1] = '
          . ${ $HoAoArrays{$key} }[$i]->[1];
    }

    say '';
}

say '', Dumper \%HoAoArrays;

__DATA__
KN-1791-LAST_rep_c7834	IMGA|Medtr4g125100.1	2e-139	497
KN-1791-LAST_rep_c7834	IMGA|Medtr4g125100.1	4e-46	187
KN-1791-LAST_rep_c7834	IMGA|Medtr4g125100.2	4e-46	187
KN-1792-LAST_rep_c7834	IMGA|Medtr4g125100.1	2e-150	497
KN-1792-LAST_rep_c7834	IMGA|Medtr4g125100.1	4e-37	187
KN-1792-LAST_rep_c7834	IMGA|Medtr4g125100.2	4e-37	187
KN-1792-LAST_rep_c7834	IMGA|Medtr4g125100.3	4e-35	188

##</code><code>##

${ $HoAoArrays{KN-1792-LAST_rep_c7834} }[0]->[1] = 2e-150
${ $HoAoArrays{KN-1792-LAST_rep_c7834} }[1]->[1] = 4e-37
${ $HoAoArrays{KN-1792-LAST_rep_c7834} }[2]->[1] = 4e-37
${ $HoAoArrays{KN-1792-LAST_rep_c7834} }[3]->[1] = 4e-35

${ $HoAoArrays{KN-1791-LAST_rep_c7834} }[0]->[1] = 2e-139
${ $HoAoArrays{KN-1791-LAST_rep_c7834} }[1]->[1] = 4e-46
${ $HoAoArrays{KN-1791-LAST_rep_c7834} }[2]->[1] = 4e-46

$VAR1 = {
          'KN-1792-LAST_rep_c7834' => [
                                        [
                                          'IMGA|Medtr4g125100.1',
                                          '2e-150',
                                          '497'
                                        ],
                                        [
                                          'IMGA|Medtr4g125100.1',
                                          '4e-37',
                                          '187'
                                        ],
                                        [
                                          'IMGA|Medtr4g125100.2',
                                          '4e-37',
                                          '187'
                                        ],
                                        [
                                          'IMGA|Medtr4g125100.3',
                                          '4e-35',
                                          '188'
                                        ]
                                      ],
          'KN-1791-LAST_rep_c7834' => [
                                        [
                                          'IMGA|Medtr4g125100.1',
                                          '2e-139',
                                          '497'
                                        ],
                                        [
                                          'IMGA|Medtr4g125100.1',
                                          '4e-46',
                                          '187'
                                        ],
                                        [
                                          'IMGA|Medtr4g125100.2',
                                          '4e-46',
                                          '187'
                                        ]
                                      ]
        };