<PAGE>   1
                                                                    EXHIBIT 10.6


                                 SEMINIS, INC.
                         SEMINIS VEGETABLE SEEDS, INC.
                                SVS HOLLAND B.V.
                SECOND AMENDMENT AND WAIVER TO CREDIT AGREEMENT



Harris Trust and Savings Bank
Chicago, Illinois


The Banks party to the Credit Agreement
  referred to below



Ladies and Gentlemen:

         Reference is hereby made to that certain Credit Agreement dated as of
June 28, 1999, as amended (the "Credit Agreement") among the undersigned,
SEMINIS, INC., a Delaware corporation ("Seminis"), SEMINIS VEGETABLE SEEDS,
INC., a California corporation ("SVS" ) and SVS HOLLAND B.V., a private company
with limited liability incorporated under the laws of The Netherlands ("SVS
Holland" and, together with Seminis and SVS, individually a "Borrower" and
collectively the "Borrowers"), you (the "Banks") and Harris Trust and Savings
Bank, as administrative agent for the Banks (the "Administrative Agent"). All
capitalized terms used herein shall have the same meaning as in the Credit
Agreement unless otherwise defined herein.

         The Administrative Agent, the Banks and the Borrowers wish to amend
certain provisions of the Credit Agreement, all in the manner set forth in this
Amendment.

1.  AMENDMENTS.

         Upon satisfaction of all of the conditions precedent set forth in
Section 3 hereof, the following provisions of the Credit Agreement shall be
amended, effective as of March 31, 2000, as follows:

        1.1. The first sentence in Section 1.8(b) of the Credit Agreement shall
be amended by adding the proviso "; provided, however, such liens and security
interests shall not be terminated or released prior to December 31, 2001"
immediately before the period at the end of the sentence thereof.

        1.2. The following definitions appearing in Section 4.1 of the Credit
Agreement shall be amended and restated in their entirety to read as follows:



<PAGE>   2



                    "Applicable Margin" shall mean with respect to the
         commitment fee and each type of Portion of the Revolving Credit Loans
         and the Term Loans described below, the rate of interest per annum
         shown below for the range of Debt Ratio specified below:

<TABLE>
<CAPTION>

                                LEVEL I       LEVEL II       LEVEL III       LEVEL IV        LEVEL V        LEVEL VI
<S>                           <C>            <C>             <C>           <C>             <C>             <C>
     Debt Ratio               < 2.50 to 1    > 2.50 to 1     >3.00 to 1    > 3.50 to 1     >3.75 to 1      >4.00 to 1
                                             -               -             -               -               -
                                             < 2.99 to 1     <3.49 to 1    < 3.74 to 1     < 3.99 to 1
                                             -               -             -               -

     Base Rate Portion            0%             0%              0%           0.25%           0.50%          0.75%

     LIBOR Portion               1.25%         1.375%          1.50%          1.75%           2.00%          2.50%

     Commitment Fee              0.25%          0.30%          0.35%          0.40%           0.50%          0.50%
</TABLE>

         provided, however, that if and so long as any Event of Default has
         occurred and is continuing, the Applicable Margins other than the
         Applicable Margin for the commitment fee as otherwise computed
         hereunder shall be increased by adding 2% per annum thereto.

                         The Applicable Margins will be adjusted upon receipt of
         Seminis' quarterly financial statements for each fiscal quarter of
         Seminis and the related Compliance Certificate, commencing with the
         quarter ended June 30, 2000. Not later than 5 Business Days after
         receipt by the Administrative Agent of the financial statements called
         for by Section 7.4 hereof for each fiscal quarter of Seminis, the
         Administrative Agent shall determine the Debt Ratio for the applicable
         period and shall promptly notify the Borrowers and the Banks of such
         determination and of any change in the Applicable Margins resulting
         therefrom. Any such change in the Applicable Margins shall be effective
         as of the date the Administrative Agent so notifies the Borrowers and
         the Banks with respect to all Loans outstanding on such date, and such
         new Applicable Margins shall continue in effect until the effective
         date of the next redetermination in accordance with this Section. Each
         determination of the Debt Ratio and Applicable Margins by the
         Administrative Agent in accordance with this Section shall be
         conclusive and binding on the Borrowers and the Banks absent manifest
         error. From June __, 2000 until the Applicable Margins are first
         adjusted pursuant hereto, the Applicable Margins shall be those set
         forth in Level VI.

                        "EBITDA" shall mean, with reference to any period, Net
         Income for such period plus all amounts deducted in arriving at such
         Net Income amount in respect of (i) Interest Expense for such period,
         plus (ii) federal, state and local income taxes for such period, plus
         (iii) all amounts properly charged for depreciation of fixed assets and
         amortization of intangible assets during such period on the books of
         Seminis and its Subsidiaries, minus (in the case of gains) or plus (in
         the case of losses) (iv) non-cash charges relating to foreign currency
         gains or losses attributable to (a) intercompany loans from Seminis and
         its Domestic Subsidiaries to Seminis' Foreign Subsidiaries and (b) any
         indebtedness of SVS Holland under this Agreement, plus (v) the
         write-off of unamortized loan origination fees associated with credit
         facilities entered into prior to the date of this Agreement, plus (vi)
         non-cash charges with respect to purchase accounting adjustments

                                      -2-

<PAGE>   3


         associated with acquisitions permitted by this Agreement, plus (vii) an
         aggregate amount of up to $19,000,000 of write-offs of non-cash
         inventory taken during Seminis' fiscal year ending September 30, 2000,
         plus (viii) an aggregate amount of up to $14,000,000 of restructuring
         charges through December 31, 2000; provided that for purposes of
         determining EBITDA for any period prior to any acquisition permitted
         hereunder the acquired entity shall be treated as though it had been a
         Subsidiary of Seminis at all times during the relevant period, and
         provided further that for purposes of determining EBITDA for any period
         prior to a disposition of any Subsidiary permitted by this Agreement
         such entity shall be treated as though it had not been a Subsidiary of
         Seminis during the relevant period.

         1.3. Section 4.1 of the Credit Agreement shall be amended by adding the
following definitions thereto in the appropriate alphabetical order:

                  "Class A Common Stock" shall mean the Class A Common Stock,
par value $.01 per share, of Seminis.

                  "Class B Preferred Stock" shall mean the Class B Redeemable
Preferred Stock, par value $.01 per share, of Seminis.

                  "Class C Preferred Stock" shall mean the Class C Redeemable
         PIK Preferred Stock, par value $.01 per share, of Seminis.

                  "Class D Preferred Stock" shall mean the Class D Redeemable
         Convertible PIK Preferred Stock, par value $.01 per share, of Seminis.

                  "Current Asset Security Agreement" shall mean the Security
         Agreement re: Accounts, Inventory and General Intangibles among the
         Domestic Borrowers and the Administrative Agent, as the same may be
         supplemented and amended from time to time.

        1.4. The definition of the term "Security Documents" appearing in
Section 4.1 of the Credit Agreement shall be amended by adding the phrase "the
Current Asset Security Agreement," immediately after the phrase "shall mean"
appearing in the first line thereof.

         1.5. Section 7.8 of the Credit Agreement shall be amended by adding the
following sentence immediately at the end thereof:

         "Notwithstanding anything contained in this Section 7.8 to the
         contrary, prior to December 31, 2001, the Borrowers will not, and will
         not permit any Subsidiary to, use, issue, incur, assume, create or have
         outstanding any Debt, nor be or remain liable, whether as endorser,
         surety, guarantor or otherwise, for or in respect of any Debt of any
         other Person in connection with any acquisition, merger or investment
         otherwise permitted under this Agreement."

                                      -3-

<PAGE>   4


         1.6. Section 7.18 of the Credit Agreement shall be amended and restated
in its entirety to read as follows:

                       "Section 7.18. Capital Expenditures. Each Borrower will
         not, and will not permit any Subsidiary to, expend for Capital
         Expenditures, net of (x) the amount of proceeds of the sale of capital
         assets of such Borrower and its Subsidiaries and (y) Capital
         Expenditures incurred in such fiscal year in connection with the
         acquisition and construction of the Oxnard Facilities in an aggregate
         of up to $30,000,000 during the term of this Agreement, in any fiscal
         year in an amount in excess of (a) $25,000,000 in each of the fiscal
         years ending September 30, 2000 and September 30, 2001, and (b)
         $40,000,000 in any fiscal year of Seminis thereafter, provided, that
         any portion of any such amount which is not expended in the fiscal year
         for which it is permitted above (commencing with the fiscal year ending
         September 30, 2001), but not to exceed $10,000,000 for any fiscal year,
         may be carried over and added to the amount which is to be available
         for expenditure by Seminis and its Subsidiaries in the next following
         year, commencing with Seminis' fiscal year ending September 30, 2002."

         1.7. Section 7.20 of the Credit Agreement shall be amended and restated
in its entirety to read as follows:

                       "Section 7.20. Minimum Interest Coverage Ratio. Seminis
         shall maintain an Interest Coverage Ratio as of the last day of each
         fiscal quarter of Seminis of not less than the ratio specified for such
         date below:
<TABLE>
<CAPTION>

                                                                    INTEREST COVERAGE RATIO
                          FISCAL QUARTER ENDING                      SHALL NOT BE LESS  THAN
                      <S>                                           <C>
                              June 30, 2000                                   2.50 to 1
                            September 30, 2000                                2.50 to 1
                            December 31, 2000                                 2.50 to 1
                              March 31, 2001                                  2.50 to 1
                              June 30, 2001                                   2.50 to 1
                            September 30, 2001                                3.00 to 1
                            December 31, 2001                                 3.50 to 1
                      March 31, 2002 and thereafter                           4.00 to 1"
</TABLE>

         1.8. Section 7.22 of the Credit Agreement shall be amended and restated
in its entirety to read as follows:

                       "Section 7.22. Maximum Debt Ratio. Seminis shall not
         permit, as of the last day of any fiscal quarter, its Debt Ratio to be
         greater than the ratio specified for such date below:

                                      -4-

<PAGE>   5
<TABLE>
<CAPTION>

                                                       DEBT RATIO SHALL NOT BE
           FISCAL QUARTER ENDING                             GREATER THAN
     <S>                                               <C>
               June 30, 2000                                  4.25 to 1
            September 30, 2000                                4.25 to 1
             December 31, 2000                                3.75 to 1
              March 31, 2001                                  4.00 to 1
               June 30, 2001                                  3.75 to 1
     September 30, 2001 and thereafter                       3.25 to 1"
</TABLE>

        1.9. Section 7.26 of the Credit Agreement shall be amended by deleting
subsections (i) and (ii) thereof and inserting the following provisions as
subsections (i), (ii), (iii) and (iv) thereof:

                  "(i) that so long as no Event of Default or Potential Default
         shall exist both before and after giving effect thereto, Seminis may
         make the following Restricted Payments:

                            (A) Seminis may pay dividends in an aggregate
                  amount of up to $2,000,000 in each year on its Class B
                  Preferred Stock;

                            (B) Seminis may pay dividends on its Class C
                  Preferred Stock so long as such dividends are paid solely in
                  additional shares of Class C Preferred Stock; and

                            (C) Seminis may pay dividends on its Class D
                  Preferred Stock so long as such dividends are paid solely in
                  additional shares of Class D Preferred Stock or shares of
                  Class A Common Stock, as the case may be;

                  (ii) so long as Seminis' financial statements as of December
         31, 2001 show that no Event of Default or Potential Default has
         occurred and is continuing, Seminis may make any Restricted Payment at
         any time after the Administrative Agent's receipt of such financial
         statements, provided, however, that no Event of Default or Potential
         Default shall exist both before and after giving effect thereto, and
         provided, further, that a minimum available amount of $75,000,000 under
         the Revolving Credit Commitments exists after giving effect thereto;

                 (iii) Seminis may redeem for cash shares of Class C Preferred
         Stock owned by Savia so long as such redemption is made solely with the
         cash proceeds of the issuance and sale of its Class D Preferred Stock
         pursuant to a rights offering registered with the Securities and
         Exchange Commission to any Person other than Savia; and

                  (iv) Seminis may redeem for cash any fractional shares
         remaining outstanding after the conversion of Class D Preferred Stock
         into Class A Common Stock, provided that the aggregate amount of all
         such redemptions shall not exceed $100,000."

                                       -5-
<PAGE>   6

         1.10. The Credit Agreement shall be amended by adding the following
provision thereto as Section 7.28 thereof:

                           "Section 7.28. Collateral of Subsidiaries. Seminis
                  will not permit its Domestic Subsidiaries (other than MBS,
                  Inc.) to have Inventory with an aggregate value (being the
                  lower of cost of market value) in excess of $5,000,000 or
                  accounts receivable in an aggregate amount in excess of
                  $5,000,000 unless such Domestic Subsidiaries have first become
                  parties to the Current Asset Security Agreement and granted to
                  the Administrative Agent for the benefit of the Banks a
                  perfected first priority security interest in such Domestic
                  Subsidiary's Collateral (as defined in the Current Asset
                  Security Agreement)."

2.  WAIVER.

         2.1. The Borrowers acknowledge that prior to giving effect to this
Amendment, Seminis is in default of its obligations under Sections 7.22 of the
Credit Agreement as of March 30, 2000 (the "Existing Default"). Upon
satisfaction of the conditions precedent set forth in Section 3 hereof, the
Required Banks hereby waive the Existing Default.

         2.2. The waiver contained in Section 2.1 of this Amendment is limited
to the matters set forth in that Section, and the Borrowers agree that they
remain obligated to comply with the terms of the Credit Agreement and the other
Loan Documents and that the Banks shall not be obligated in the future to waive
any provision of the Credit Agreement or the other Loan Documents as a result of
having provided the waiver contained herein.

3.  CONDITIONS PRECEDENT.

         This Amendment shall become effective upon the satisfaction of all of
the following conditions precedent:

         3.1. The Administrative Agent, the Banks and the Borrowers shall have
executed and delivered this Amendment.

         3.2. The Administrative Agent, Seminis and SVS shall have executed and
delivered the Security Agreement re: Accounts, Inventory and General
Intangibles.

         3.3. The Administrative Agent shall have received for the ratable
benefit of the Banks that execute this Amendment (the "Approving Banks") an
amendment fee in an amount equal to three-eighths of one percent (0.375%) of the
maximum amount of the Exposure of each of the Approving Banks.

         3.4. Seminis shall have issued to Savia its Class C Preferred Stock in
exchange for the satisfaction in full of intercompany loans and advances in an
aggregate principal amount of

                                      -6-
<PAGE>   7


$42,000,000 plus accrued and unpaid interest thereon previously made by Savia to
Seminis, all on terms and conditions acceptable to the Administrative Agent.

         3.5. Each of the representations and warranties set forth in Section 5
of the Credit Agreement shall be and remain true and correct as to each of the
Borrowers, except that the representations and warranties made under Section 5.2
(except the last sentence thereof) shall be deemed to refer to the most recent
financial statements furnished to the Banks pursuant to Section 7.4 of the
Credit Agreement.

         3.6. No Potential Default or Event of Default shall have occurred and
be continuing.

4.  REPRESENTATIONS AND WARRANTIES.

         The Borrowers represent and warrant to the Administrative Agent and the
Banks as follows:

        4.1. Each of the representations and warranties set forth in Section 5
of the Credit Agreement are true and correct as to each of the Borrowers as of
the effective date hereof, except that the representations and warranties made
under Section 5.2 (except the last sentence thereof) shall be deemed to refer to
the most recent financial statements furnished to the Banks pursuant to Section
7.4 of the Credit Agreement.

        4.2. The Borrowers are in full compliance with all of the terms and
conditions of the Loan Documents and no Event of Default or Potential Default
shall have occurred and be continuing thereunder or shall result after giving
effect to this Amendment.

5.  MISCELLANEOUS.

        5.1. The Borrowers have heretofore executed and delivered to the
Administrative Agent certain Security Documents, and the Borrowers hereby agree
that the Security Documents shall secure all of the Borrowers' indebtedness,
obligations and liabilities to the Administrative Agent and the Banks under the
Credit Agreement as amended by this Amendment, that notwithstanding the
execution and delivery of this Amendment, the Security Documents shall be and
remain in full force and effect and that any rights and remedies of the
Administrative Agent thereunder, obligations of the Borrowers thereunder and any
liens or security interests created or provided for thereunder shall be and
remain in full force and effect and shall not be affected, impaired or
discharged thereby. Nothing herein contained shall in any manner affect or
impair the priority of the liens and security interests created and provided for
by the Security Documents as to the indebtedness which would be secured thereby
prior to giving effect to this Amendment.

        5.2. Reference to this specific Amendment need not be made in any note,
document, letter, certificate, the Credit Agreement itself, or any communication
issued or made pursuant to or with respect to the Credit Agreement, any
reference to the Credit Agreement being sufficient to refer to the Credit
Agreement as amended hereby.

                                      -7-
<PAGE>   8

        5.3. This Amendment may be executed in any number of counterparts, and
by the different parties on different counterparts, all of which taken together
shall constitute one and the same agreement. Any of the parties hereby may
execute this Amendment by signing any such counterpart and each of such
counterparts shall for all purposes be deemed to be an original. This Amendment
shall be governed by the internal laws of the State of Illinois.


                                      -8-
<PAGE>   9

         Upon acceptance hereof by the Administrative Agent and the Banks in the
manner hereinafter set forth, this Amendment shall be a contract between us for
the purposes hereinabove set forth.

         Dated as of June ___, 2000 but effective as of March 31, 2000.


                             SEMINIS, INC.



                             By
                                Its
                                   ---------------------------------------------


                             SEMINIS VEGETABLE SEEDS, INC.



                             By
                                Its
                                   ---------------------------------------------


                             SVS HOLLAND B.V



                             By
                                Its
                                   ---------------------------------------------

                                      -9-
<PAGE>   10

         Accepted and agreed to as of the day and year last above written.


                                   HARRIS TRUST AND SAVINGS BANK,
                                      individually and as Administrative Agent



                                   By
                                      Its Vice President


                                   CREDIT AGRICOLE INDOSUEZ


                                   By
                                      Its
                                         ---------------------------------------



                                   By
                                      Its
                                         ---------------------------------------


                                   BANK OF AMERICA, N.A.



                                   By
                                      Its
                                         ---------------------------------------


                                   THE BANK OF NOVA SCOTIA



                                   By
                                      Its
                                         ---------------------------------------


                                   COMERICA BANK



                                   By
                                      Its
                                         ---------------------------------------


                                   BANK ONE, NA



                                   By
                                      Its
                                         ---------------------------------------

                                      -10-
<PAGE>   11

                                   BNP PARIBAS



                                   By
                                      Its
                                         ---------------------------------------



                                   By
                                      Its
                                         ---------------------------------------



                                   UNION BANK OF CALIFORNIA, N.A.



                                   By
                                      Its
                                         ---------------------------------------


                                   FLEET NATIONAL BANK



                                   By
                                      Its
                                         ---------------------------------------


                                   MEESPIERSON CAPITAL CORP.



                                   By
                                      Its
                                         ---------------------------------------


                                   RABOBANK INTERNATIONAL



                                   By
                                      Its
                                         ---------------------------------------


                                   SANWA BANK CALIFORNIA



                                   By
                                      Its
                                         ---------------------------------------

                                      -11-
<PAGE>   12

                                   THE FUJI BANK, LIMITED



                                   By
                                      Its
                                         ---------------------------------------


                                   THE MITSUBISHI TRUST & BANKING CORPORATION



                                   By
                                      Its
                                         ---------------------------------------


                                   US BANCORP AG CREDIT, INC.



                                   By
                                      Its
                                         ---------------------------------------


                                   THE DAI-ICHI KANGYO BANK, LTD.



                                   By
                                      Its
                                         ---------------------------------------



                                      -12-