quantitative genetics of rice

8/2/2019 Quantitative Genetics of Rice

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E L S E V I E R Field Crops Research 55 (1998) 275-281

F i e l dC r o p sR e s e a r c h

Q uantitat ive gen et ics o f r iceIV. A breeding strategy

M . J . L a w r e n c e a ,* , D . S e n a d h i r a ba Wol fson Laboratory fo r P lan t Mo lecular B iology, Schoo l of B iological Sciences , Univers ity of B irmingham, B irmingham B 15 2TT, UK

b P lant Breeding, Genet ics and B iochem is try Division, Internat ional R ice Research Inst itu te , PO Bo x 933, Man i la 1099, Phi l ippinesRece ived 28 M arc h 1997; revised 22 July 1997; accepted 23 July 1997

A b s t r a c t

A sys t em at i c and o b j ec t i ve b reed i ng s t r a t egy i s p roposed , i nvo l v i ng t h r ee s t ages o f se l ec t i on car r i ed ou t a t t he F 1 , F 3 andF6 genera t i ons o f ped i g re es founded on s i ng l e c ro sses be t ween i nb red paren t s . The f i r s t t wo o f t hese s t ages i nvo l ve se l ec t i onbe t we en pe d i g rees and t he t h i rd , se l ec t i on wi t h i n t he ped i g re es t ha t su rv i ve the f i r s t two s t ages o f sc ru t i ny . The key f ea t u reso f t h i s p rocedu re a r e : tha t se l ec t i on wi t h i n ped i g rees i s de l ay ed un t i l i nd i v i dua l s a r e e f f ec t i ve l y hom ozygo us ; t ha t a l lcharac t e r s a r e measu red d i r ec t l y ; and t ha t dec i s i ons a r e based on t he per fo rmance o f p l an t s t ha t a r e r a i sed i n r ep l i ca t ed andr a n d o m i s e d t r i a l s . T h e r e p l a c e m e n t o f t h e p e d i g r e e m e t h o d b y t h e n e w m e t h o d s h o u l d a l l o w b r e e d e r s t o r e c o g n i s e a n dexp l o i t t he gene t i ca l var i a t i on be t ween and w i t h i n t he i r c ro sses fo r charac t e r s o f i n t e r es t more e f f i c i en t l y t han h i t her t o a t ana p p r e c i a b l y lo w e r c o s t . W h i l e t h is n e w m e t h o d h a s b e e n p r o p o s e d i n r e s p o n s e t o a s p e c i fi c p r o b l e m w i t h r i c e, i t i s a p p l i c a b let o a l l c rop p l an t spec i es where t he end p roduc t s o f b r eed i ng p rog rammes a r e i nb red l i nes . 1998 El sev i e r Sc i ence B .V .K eyw ords : Biom etrical breeding m ethod; Self-pollinating crops

I . I n t r o d u c t i o n

W e h a v e s h o w n t h a t t h e re i s n o e v i d e n c e o f as h o r t a g e o f a d d i t i v e g e n e t i c a l v a r i a t i o n f o r y i e l d a n do t h e r c h a r a c t e rs o f a g r o n o m i c i m p o r t a n c e a m o n gm o d e m i n d i c a c u l t i v a r s o f ri c e t h a t h a v e b e e n b r e df o r u s e i n t r a n s p l a n t e d c r o p s i n t h e l o w l a n d t r o p i c s( P e r e r a e t a l ., 1 9 98 ) . O n e o f t he c h i e f c a u s e s o f t h ei n a b i l i t y o f b r e e d e r s t o i n c r e a s e t h e y i e l d p o t e n t i a l o fc u l t i v a r s o f I R 8 i d e o t y p e o v e r t h e l a s t 3 0 y e a r s( F l i n n e t a l ., 1 9 8 2 ; C a s s m a n e t a l. , 1 9 9 4 ) i s , t h e r e -f o r e , th e u s e o f b r e e d i n g m e t h o d s t h a t fa i l t o e x p l o i t

* Corresponding author. Tel .: +44-121-414-5915; fax: +4 4-121-414-5925.

t h e g e n e t i c a l v a r i a t i o n t h a t i s p r e s e n t i n t h e i r c ro s s e s .T h e r e s u l t s o b t a i n e d b y F a h i m e t a l . ( 1 9 9 8 ) s u p p o r tt h i s c o n c l u s i o n . T h u s , n o n e o f t h e b e s t F 6 l i n e sp r o d u c e d b y a n y o f t h e th r e e m e t h o d s i n w h i c hs e l e c t i o n w a s p r a c t i s e d f o r y i e l d d u r i n g t h e c o u r s e o fi n b r e e d in g , t h e p e d i g r e e , m o d i f i e d p e d i g r e e a n d b u l km e t h o d s , w e r e s i g n i f i c a n t l y b e t t e r th a n t h e b e s t l i n e sp r o d u c e d b y s i n g l e s e e d d e s c e n t i n e i t h e r o f t h ec r o s s e s i n v e s t i g a t e d . T h e r e i s l i t tl e d o u b t , t h e r e f o r e ,t h a t s e l e c t i o n f o r y i e l d in t h e e a r l y g e n e r a t i o n s o ft h e s e p e d i g r e e s h a s n o t b e e n v e r y e f f e c t i v e . T h ei n a b i l i t y o f b r e e d e r s t o b r e a c h a n a p p a r e n t y i e l dp o t e n t i a l b a r r i e r o f 1 0 t / h a ( P e n g e t a l ., 1 9 9 4 ) w i t hi n d i c a c u l t i v a r s i s , t h u s , a l m o s t c e r t a i n l y d u e , i n p a r ta t l e a s t , t o t h e i r u s e o f i n e f f i c i e n t b r e e d i n g p r o c e -d u r e s .

0378-4290/98/$19.00 1998 Elsevier Science B.V . All rights reserved.P II S 0 3 7 8 - 4 2 9 0 ( 9 7 ) 0 0 0 8 8 - 9


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276 M.J. Lawrence, D. Senadhira / Field Crops Research 55 (1998) 275-281

I n p r e v i o u s p a p e r s , w e h a v e s h o w n h o w i n f o r m a -t io n f r o m t h e F 3 g e n e r a ti o n o f a p e d i g r e e c a n b e u s e dt o a s s e s s t h e p o t en t i a l o f a c ro s s (Pe re r a e t a l ., 1 9 9 8 ;Fah i m e t a l . , 1 9 9 8 ; Ben t o t a e t a l . , 1 9 9 8 ) w i t h r e s p ec tt o o n e o r mo re ch a rac t e r s . I t i s o b v i o u s l y i mp rac t i -ca l , h o w ev e r , t o ex p ec t b r eed e r s t o ad v an ce a l l o f ,s ay , 5 0 c ro s s e s t o t h e F 3 g en e ra t i o n t o a s s e s s t h e i rp o t en t i a l . I n t h e p r e s en t p ap e r , w e i n t ro d u ce a n ewb r e e d i n g p r o c e d u r e , d e r i v e d f r o m t h e r e s u l t s a n dc o n c l u s i o n s o b t a i n e d f r o m t h e a n a l y s e s r e p o r t e d i nt h e p r ev i o u s p a p e r s o f th i s s e r i e s, w h i ch a l l o w s t h ep o t e n t ia l o f c r o s s e s t o b e a s s e s s e d a n d r a n k e d i n ac o m p l e t e l y s y s t e m a t i c a n d o b j e c t i v e w a y .

2 . T h e n e w p r o c e d u r eT h e n e w p r o c e d u r e i n v o l v e s th r e e s t a g e s o f s e le c -

t ion c ar r i ed ou t a t the F~, F 3 and F6 g en e ra t i o n s o fp ed i g ree s t h a t a r e fo u n d ed f ro m a s i n g l e c ro s s b e -t w e e n t w o h o m o z y g o u s p a r e n t s . T h e f i r s t t w o s t a g e si n v o l v e d i s c r i m i n a t i o n b e t w e e n p e d i g r e e s a n d t h et h i rd , s e l ec t i o n w i t h i n t h e p ed i g ree s t h a t h av e s u r -v i v ed t h e f i r s t t w o s t ag es o f s c ru t i n y .2.1. The F 1 stage

T h e m o s t p r o m i s i n g c r o s s e s a r e t h o s e i n w h i c ht h e p a r e n t s a r e i d e n t i c a l l y h o m o z y g o u s f o r m o s t o ft h e i n c r ea s i n g g en es d e t e rmi n i n g t h e ch a rac t e r ( e . g . ,y i e l d ) , b u t d i f f e r f o r a mi n o r i t y t h a t a r e p a r t i a l l yd i s p e r s e d b e t w e e n t h e m , b e c a u s e i n t h e s e c i r c u m -s t a n c e s i t s h o u l d b e p o s s i b l e t o e x t r a c t r e c o m b i n a n ti n b r e d l i n e s f r o m t h e m t h a t o u t p e r f o r m t h e b e t t e rp a r e n t . P a r e n t s t h a t a r e h o m o z y g o u s f o r m a n y i n -c r ea s i n g g en es can , o f co u r s e , b e i d en t i f i ed f ro mt h e i r m e a n p e r f o r m a n c e ; t h o s e t h a t d i f f e r f o r a m i -n o r i t y o f i n c r ea s i n g g en es t h a t a r e p a r t i a l l y d i s p e r s edb e t w e e n t h e m , c a n b e r e c o g n i s e d b y t h e i r h e t e r o t i cF 1 p r o g e n y . T h u s , i n t h e a b s e n c e o f o v e r d o m i n a n c e ,t w o c o n d i t i o n s h a v e t o b e m e t f o r b e t t e r p a r e n th e t e ro s i s t o o ccu r : f i r s t , th a t t h e g en e s co n t ro l l i n g t h ech a rac t e r d i s p l ay d i r ec t i o n a l d o mi n an ce , an d s eco n d ,t h a t t h o s e o f s i mi l a r d i r ec t i o n a l e f f ec t a r e d i s p e r s edb e t w een t h e p a r en t s . I f , t h e r e fo re , t h e F 1 o f a c ro s sd i s p l ay s h e t e ro s i s , a t l e a s t s o me o f t h e g en es fo rw h i c h t h e p a r e n t s d i f f e r m u s t b e d i s p e r s e d b e t w e e nt h em; t h a t i s , h e t e ro s i s i n d i ca t e s t h i s d i s p e r s i o n .

D o mi n an ce a s s u ch i s o f l i t t l e i n t e r e s t t o t h e b r eed e ro f s m a l l - g r a i n c e r e a l s , b e c a u s e t h e p r o d u c t s o f t h e i rb r e e d i n g p r o g r a m m e s a r e h o m o z y g o u s l i n e s . H e r e , i ts e r v e s a s n o m o r e t h a n a m e a n s o f d e te c t in g d i s p e r -s i o n . I t i s , o f co u r s e , p o s s i b l e t h a t t h e g en es fo rw h i ch t h e p a r en t s d i f f e r , a l t h o u g h d i s p e r s ed b e t w eent h em, d o n o t d i s p l ay d i r ec t i o n a l d o mi n an ce ; s i n ce , i nt h e s e c i r cu ms t an ces , t h e i r F~ i s n o t ex p ec t ed t o d i s -p l a y h e t e r o s i s , s u c h c r o s s e s m i g h t b e o v e r l o o k e d .T h e emp i r i ca l ev i d en ce , h o w ev e r , s u g g es t s t h a t t h i si s u n l i k e l y . T h u s , i n t h e t w o i n v es t i g a t i o n s i n w h i cht r i p l e t e s t c ro s s p ro g en i e s w e re r a i s ed , ( t h e o n l yd e s i g n y i e l d i n g i n d e p e n d e n t e s t i m a t e s o f t h e d o m i -n a n c e c o m p o n e n t o f v a r i a t i o n , H ) , t h e m a j o r i t y o ft h e ch a rac t e r s r eco rd ed , i n c l u d i n g y i e l d an d i t s co m-p o n e n t s , d i s p l a y e d d o m i n a n c e i n t h e e i g h t c r o s s e san a l y s ed , w h i ch fo r mo s t , h ad a d i r ec t i o n a l e l em en t(Pe rera e t a l ., 1998) . A t r i a l o f paren t s a nd the i r F 1p ro g en y s h o u l d , t h e r e fo re , a l l o w t h e b r eed e r t o i d en -t i fy t h e m o s t p r o m i s i n g c r o s s e s o f a c o h o r t.

I t i s e s s en t i a l , h o w ev e r , t h a t t h i s t r i a l s h o u l d b eap p ro p r i a t e l y r an d o m i s ed , an d t h a t p l an t s s h o u l d b emeas u red fo r ch a rac t e r s o f i n t e r e s t , y i e l d , f o r ex am-p l e , b e i n g r e c o r d e d a s t h e a m o u n t o f g r a i n p r o d u c e db y t h e p l an t s o f e ach f ami l y i n t h e t r i a l . A l t h o u g hp l a n t s w e r e r a i s e d i n c o m p l e t e l y r a n d o m i s e d d e s i g n si n o u r ex p e r i men t s , b r eed e r s w i l l p ro b ab l y f i n d i tmo re co n v en i en t t o r a i s e t h e i r s i n s ma l l p l o t s , w h i chh a v e t h e a d d i t i o n a l a d v a n t a g e o f a v o i d i n g c o m p e t i -t io n b e t w e e n p l a n t s o f d i f f e r en t g e n o t y p e . S u p p o s e ab reed e r s t a r t s w i t h 5 0 c ro s s e s i n v o l v i n g 1 0 0 d i f f e r en tp a ren t s . T h en , a d e s i g n i n w h i ch each o f t h e 1 5 0fami l i e s i s r ep re s en t ed b y a p a i r o f p l o t s co n t a i n i n g1 0 p l an t s , w h o s e p o s i t i o n i n t h e t r i a l i s a s s i g n ed a tr a n d o m , w o u l d g i v e u n b i a se d e s t i m a t e s o f t h e m e a n so f t h e s e f am i l i e s , an d w o u l d a l l o w s t a t i s ti c a l te s t s tob e ca r r i ed o u t b e t w een t h e p a r en t s an d t h e i r F lp ro g en i e s . I t i s p o s s i b l e , h o w ev e r , t h a t p l o t s o f t h i ss i ze a r e k n o w n t o b e p o o r p r e d i c to r s o f p e r f o r m a n c eo f p l an t s i n l a rg e r p l o t s i n w h i ch i n d i v i d u a l s a r era i se d a t agr icu l tu ra l de ns i t i es . I f th is i s the case , i tw o u l d b e n eces s a ry t o i n c r ea s e t h e s i ze o f t h e p l o t si n t h is y i e l d t r ia l . T h e d i s ad v a n t ag e o f i n c r ea s i n g p l o ts i ze i s t h a t , w h i l e t h e amo u n t o f p a r en t a l s eed av a i l -ab l e i s u n l i k e l y t o b e a l i mi t i n g f ac t o r , t h a t u s ed t or a i s e t h e F l p ro g en i e s co u l d b e , b ecau s e t h i s s eedh a s t o b e p r o d u c e d b y e m a s c u l a t i o n a n d h a n d - c r o s s -ing .


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M.J. Lawrence, D. Senadhira / Field Crops Research 55 (1998) 275 -281 277As at this first stage of selection, five of the

crosses, perhaps, will be retained and the rest dis-carded.2 . 2 . T h e F 3 s t a g e

An analysis of the F 3 families of a pedigreeprovides information about four points concerningthe potential of the cross. First, an analysis of vari-ance of the data from these families allows thebreeder to find out whether all characters of interestare heritable; if it turns out that one or more charac-ters are not heritable, the cross is obviously inca-pable of yielding transgressive segregants for thesecharacters. Second, examination of the F 3 familymeans may reveal some that achieve the desiredtarget for one or more characters. A cross that ex-hibits transgressive variation as early as the F 3 gen-eration has obvious potential, since it will certainlydo so in later generations of the pedigree. Third,given that a character is heritable and normallydistributed, estimates of the mean, m, and additivegenetical variance, D, of the distribution of recombi-nant inbred lines that can be extracted by single seeddescent from the cross obtained from these families,can be used to predict the proportion of such lineswhose means equal or exceed the desired target foreach character in turn (Jinks and Pooni, 1976, 1980).If the probability of obtaining a line of the desiredlevel of performance for an important character ap-pears to be small ( < 5%), the breeder can eitherincrease the number of single seed descent linesextracted from the cross (> 100), to compensate forthis low probability, or discard the cross. Fourth, thecomponents of covariance analyses carried out on allpairs of characters can be used to estimate the ge-netic correlations between these characters. It hasbeen argued by some that the chief cause of geneticcorrelation between characters in crop plant speciesis pleiotropy (e.g., Simmonds, 1979). However, apartfrom a small number of obvious pleiotropic relation-ships, such as that between, for example, tiller andpanicle number, we have found that the pattern ofgenetic correlations varies considerably over crosses(Perera, 1985; Fahim, 1995; Sriyoheswaran, 1995;Bentota et al., 1998). This suggests that in rice, atleast, the chie f cause of these correlations is thelinkage disequilibrium of genes that are linked in

their inheritance. This being the case, it is possible toidentify crosses where the genetic correlations arefavourable to the breeder's objectives; for example,crosses in which the genetic correlations betweencharacters for which greater expression is requiredare large and positive, are more likely to yieldrecombinant inbred lines that meet the targets for allof these characters, than those in which these correla-tions are zero or negative. A knowledge of thegenetic correlations between characters, therefore,can assist the breeder in achieving the targets for allcharacters of interest, and crosses can be ranked onthis information, as well as on their potential inrespect of single characters.

As at the F 1 stage, it is essential that the individu-als of the F 3 families should be raised in a ran-domised trial, and that characters should be mea-sured and not assessed by eye. Each of the crosseswhich survive the F 1 stage should be represented by30-40 families that are raised in the same trial.Assuming, again, that breeders would find it conve-nient to raise these families in plots, each familycould be represented by a pair of independentlyrandomised plots containing, say, 10 plants. Dupli-cate plots of each of the parents should also beincluded in the trial. Alternatively, where the perfor-mance of recommended varieties of the appropriateage class is to be used to provide the targets forimprovement, duplicate plots of these should beraised instead.

It is difficult to forecast how many of thesecrosses will survive scrutiny at the F 3 stage of theprogramme, but, perhaps, the most promising pairmight be retained and the rest discarded.2 . 3 . T h e F 6 s t a g e

The design of the F6 trial can be similar to that ofthe F 3 families, each f amily being represented by apair of independently randomised 10 plant plots; thetrial should also include duplicate plots of the par-ents of each cross or of recommended varieties,where these are used to provide targets for improve-ment. The number of families to be included in thistrial requires, however, consideration. Thus, whilethe single character predictions made on the informa-tion obtained from F 3 families can be used to suggestthe number of F6 families that need to be raised inthe trial to give a reasonable chance of obtaining at


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27 8 M.J. Law rence, D. Senadhira Field Crops Research 55 (1998) 275-281l e a s t o n e t h a t m e e t s t h e d e s i r e d t a r g e t f o r e a c hc h a r a c t e r , b r e e d e r s w i l l n e a r l y a l w a y s w a n t t o i m -p r o v e a t l e a s t s e v e r a l c h a r a c t e r s s i m u l t a n e o u s l y . I np r i n c i p l e , i t i s p o s s i b l e t o c a l c u l a t e t h e p r o p o r t i o n o fr e c o m b i n a n t i n b r e d l i n e s t h a t m e e t t h e d e s i r e d t ar -g e t s f o r a n y n u m b e r o f c h a r a c t e r s; P o o n i a n d J i n k s( 1 9 7 8 ) h a v e s h o w n h o w t h i s c a n b e d o n e f o r t w o a n dt h r e e c h a r a c t e r s s i m u l t a n e o u s l y , w h i c h t a k e i n t o a c -c o u n t t h e g e n e t i c c o r r e l a t i o n s b e t w e e n c h a r a c t e r s .T h e c a l c u l a t i o n s i n v o l v e d , h o w e v e r , a r e r a t h e r t e -d i o u s a n d a r e , f o r t h is r e a s o n , u n l i k e l y t o b e w i l l -i n g l y u n d e r t a k e n b y b r e e d e r s . I n a n y c a s e , t h e c h i e fp r o b l e m t h a t f a c e s t h e b r e e d e r i s t h a t, u n l e s s t h en u m b e r o f c o m p o n e n t c h a r a c t e r s in t h e a g g re g a t ep h e n o t y p e a r e f e w , t h e p r o b a b i l i t y o f o b t a i n i n g a l i n et h a t m e e t s t h e t a r g e t s f o r a l l i s v e r y s m a l l . S u p p o s e ,f o r e x a m p l e , t h a t t h e r e a r e t h r e e c o m p o n e n t s , x , ya n d z , o f t h e a g g r e g a t e p h e n o t y p e , f o r e a c h o f w h i c hi n c r e a s i n g e x p r e s s i o n i s d e s i r e d . S u p p o s e , f u r t h e r ,t h a t t h e s e c h a r a c t e r s a r e c o m p l e t e l y u n c o r r e l a t e d .T h e n t h e p r o p o r ti o n o f re c o m b i n a n t i n b r e d l i ne s , P ,t h a t a r e e x p e c t e d t o a c h i e v e t h e t a r g e t s f o r a l l t h r e ec o m p o n e n t s s i m u l t a n e o u s l y is s i m p l y t he p r o d u c t o ft h e t h r e e s i n g l e c h a r a c t e r p r e d i c t i o n s ; t h a t i s , P =Px Py Pz . S u p p o s e P x = P y = e z = 0 . 2 o r 2 0 % ; t h e nP = 0 . 0 0 8 o r 0 .8 % a n d i t w o u l d b e n e c e s s a r y to r a is en o t l e s s th a n 5 7 0 l i n e s t o b e 9 9 % c e r t a i n o f o b t a i n i n ga t l e a s t o n e t h a t a c h i e v e d a l l t h r e e t a r g e t s s i m u l t a n e -o u s l y . I f , o n t h e o t h e r h a n d , t h e g e n e t i c c o r r e l a t i o n sb e t w e e n t h e s e c h a r a c t e r s w e r e p o s i t i v e , th e p r o p o r -t i o n o f l i n e s t h a t a c h i e v e d a l l t h r e e t a r g e t s i s e x -p e c t e d t o b e l a r g e r t h a n 0 .8 % b y a n a m o u n t t h a td e p e n d s o n t h e m a g n i t u d e o f t h e s e c o r re l a t i on s ; t hi s

i s w h y a k n o w l e d g e o f t h e g e n e t i c c o rr e l a ti o n s b e -t w e e n c h a r a c t e r s i s u s e f u l i n a q u a l i t a t i v e s e n s e , a tl e a s t , i n a s s e s s i n g t h e o d d s o f o b t a i n i n g a l i n e t h a tm e e t s a l l o f t h e d e s i r e d t a rg e t s . T h i s p r o b l e m o fa c h i e v i n g t h e t a rg e t s f o r a ll c o m p o n e n t s o f t h e d e -s i re d a g g r e g a t e p h e n o t y p e i n a s i n g l e r e c o m b i n a n ti n b r e d l i n e i s, o f c o u r s e , c o m m o n t o a l l b r e e d i n gp r o g r a m m e s , a n d i s a l m o s t c e r t a in l y a s im p o r t a n t ac a u s e o f t h e f a i l u re to b r e a c h t h e a p p a r e n t 1 0 t / h ay i e l d b a r r i e r w i t h i n d i c a c u l t i v a r s a s t h e i n e f f i c i e n te x p l o i t a t i o n o f t h e g e n e t i c a l v a r i a t i o n f o r t h e s e c o m -p o n e n t s . T h e c o n c l u s i o n h e r e i s o b v i o u s , n a m e l y ,t h a t i f b r e e d e r s w a n t t o m a x i m i s e t h e c h a n c e o fo b t a i n i n g o n e o r m o r e l i n e s t h a t a c h i e v e a l l o f t h ed e s i r e d t a r g e t s w i t h o n e c y c l e o f i n b r e e d i n g , t h e ys h o u l d r a i s e a s m a n y f a m i l i e s i n t h e F 6 t r i a l as t h e i rr e s o u r c e s a l l o w .2 . 4 . L o g i s t i c a l c o n s i d e r a t i o n s

A s w i t h a l l b r e e d i n g p r o g r a m m e s , t h e i m p l e m e n -t a t i o n o f t h i s p r o c e d u r e w i l l i n v o l v e s o m e c a r e f u lp l a n n i n g . I t is a s s u m e d t h a t w h i l e b r e e d e r s w i l l w a n tt o c a r r y o u t t h e F l , F 3 a n d F 6 t r ia l s i n t h e d r y s e a s o n ,t h e p r o d u c t i o n o f s e e d , i n c l u d i n g t h a t o f t h e s i n g l es e e d d e s c e n t l i n e s , c a n b e c a r r i e d o u t a t a n y t i m e o ft h e y e a r i n t he n u r s e r y . I t s h o u l d b e p o s s i b l e , t h e re -f o r e , to c a r r y o u t a c o m p l e t e c y c l e o f t h e p r o c e d u r ew i t h i n a p e r i o d o f t h re e y e a r s a s s h o w n i n T a b l e 1 .T h e n u m b e r o f p la n t s s h o w n i n t h e l a st c o l u m n o ft h i s t a b l e a s s u m e s t h a t t h e p r o g r a m m e i s i n i t i a t e dw i t h 5 0 c r o s s e s , t h a t t h e b e s t f i v e o f t h e s e a r ea d v a n c e d t o t h e F 3 g e n e r a t i o n a n d t h a t t w o o f t h e s e

Table 1A summary of the new breeding methodYear Season Generation Task

Nursery FieldNo. of plots Total no.in trials of plants1 W et Parents Production - - 100of F1 seed

Dry F 1 - F trial and 300 3000production of F2 seed2 Wet F2 Production - - 2500o f F3 seedDry F3 SSD ~ F 4 F 3 trial 400 2500 + 40003 - F4 SSD ~ F5 - - 1000- - F5 SSD ~ F6 - - 1000- Dry F6 - F6 trial 2000 20,000


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M.J. Lawrence, D. Senadhira / Field Crops Research 55 (1998) 275-281 279a r e a d v a n c e d t o t h e F 6 g en e ra t i o n . I t i s f u r t h e ra s s u m e d t h a t e a c h f a m i l y i s r e p r e s e n te d b y 1 0 p la n t si n e a c h o f a p a i r o f i n d e p e n d e n t l y r a n d o m i s e d p l o t si n each o f t h e t h r ee t r i a l s ; t h a t 4 0 f ami l i e s a r e r a i s edi n each c ro s s i n t h e F 3 t r ia l ; an d t h a t 5 0 0 s i n g l e s eedd es cen t l i n e s a r e r a i s ed i n each c ro s s i n t h e F6 t r ial .T h e n u m b e r o f p l o t s r a i s e d i n e a c h o f t h e t r i a l s ,s h o w n i n th e p e n u l t i m a t e c o l u m n o f T a b l e 1 , i n d i-c a t e s t h e s i z e s o f t h e r a n d o m p e r m u t a t i o n s r e q u i r e dt o r an d o mi s e t h e s e t r i a l s .

T o en s u re t h a t t h e s i n g l e s eed d es cen t l i n e s a r ea d v a n c e d t o t h e F6 g e n e r a t i o n b y t h e d r y s e a s o n o ft h e t h ir d y e a r o f t h e p r o g r a m m e , i t w i l l b e n e c e s s a r yt o i n i t i a t e t h e s i n g l e s eed d es cen t p h as e o f t h e p ro -g ra m m e a s s o o n a s F 2 s eed i s av a i l ab l e , t h a t i s ,b e fo re t h e r e s u l t s o f t h e F 3 t r i a l a r e av a i l ab l e . H en ce ,i t w i l l b e n eces s a ry t o i n i t i a t e s i n g l e s eed d es cen t f o reach o f t h e f i v e c ro s s e s i n t h i s t r i a l . O n ce , h o w ev e r ,t h e b e s t p a i r o f c ro s s e s h av e b een i d en t i f i ed i n t h i st r i a l , a t t en t i o n can b e co n cen t r a t ed o n ad v an c i n gt h em as q u i ck l y a s p o s s i b l e t o t h e F 6 g en e ra t i o n an dt h e l i n e s o f t h e r ema i n i n g t h r ee c ro s s e s d i s ca rd ed .A g a i n , w h i l e t h e p l an t s o f th e ea r l y g en e ra t i o n s o ft h e s i n g l e s e e d d e s c e n t p h a s e o f t h e p r o g r a m m e c a nb e r a i s ed a t h i g h d en s i t i e s i n t r ay s i n t h e n u r s e ry , i tw i l l b e n ece s s a ry t o r a i s e t h o s e o f t h e F 5 g en e ra t i o na t a l o w e r d e n s i t y t o e n s u r e t h a t t h e y p r o d u c e e n o u g hg o o d s e e d f o r t h e F6 t r ial .

3 . D i s c u s s i o nT h e k e y f e a t u r e s o f t h is n e w p r o c e d u r e h a v e

e m e r g e d f r o m t h e i n v e s ti g a t io n s r e p o r t e d i n p r e v i o u sp ap e r s o f t h i s s e r ie s (Pe re r a e t a l . , 1 9 9 8 ; Fah i m e t a l. ,1998 ; Ben to ta e t a l . , 1998) ; i t i s , therefore , wel lfo u n d ed o n b o t h q u an t i t a t i v e g en e t i c s t h eo ry an d t h ee m p i r i c a l e v i d e n c e . B e c a u s e , h o w e v e r , i t i n v o l v e s ar a d i c al d e p a r t u r e f r o m c u r r e n t p ra c t ic e , b r e e d e r s m a yi n i t i a l l y b e r e l u c t an t t o u s e t h i s p ro ced u re . I t i sw o r t h w h i l e , t h e r e fo re , r e i t e r a t i n g t h e i mp o r t an ce o ft h e t h r e e c h i e f w a y s i n w h i c h t h is p r o c e d u r e d i f f e r sf r o m c o n v e n t i o n a l m e t h o d s .

T h e f i r s t o f t h e s e i s th a t s e l ec t i o n w i t h i n p ed i g re e si s d e f e r r ed u n t i l t h e F6 gen era t ion , the F~ and F 3s t a g e s o f t he p r o c e d u r e b e i n g u s e d s o l e ly t o d i s c r im i -n a t e b e t w e e n c r o s s e s . W i t h t h e p e d i g r e e m e t h o d , o nt h e o t h e r h an d , s e l ec t i o n i s p r ac t i s ed f ro m t h e F 2g en e ra t i o n o n w ard s , i n i t i a l l y o n s i n g l e p l an t p e r fo r -

m a n c e a n d l a t e r o n f a m i l y m e a n s . O n t h e o r e t i c a lg ro u n d s , t h i s s e l ec t i o n can n o t b e v e ry e f f i c i en t b e -cau s e t h e h e r i t ab i li t ie s o f ch a rac t e r s o f i n t e r e s t a r e , a tb e s t u s u a l l y o n l y m o d e r a t e . T h e e s t i m a t e s o f t h eh e r i t ab i l i t y o f g r a i n y i e l d i n t h e c ro s s e s i n v es t i g a t edb y Pe re r a e t a l . ( 1 9 9 8 ) , f o r ex amp l e , w e re 1 6 % an d1 1 % , f o r t h o s e in e x p e r i m e n t 2, a n d 3 1 % , 4 4 % a n d4 3 % , fo r t h o s e i n ex p e r i men t 3 , t h e l a t t e r p a i r o fe s t im a t e s b e i n g u n u s u a l l y h i g h . E s t i m a t e s o f t h e s em a g n i t u d e s i n d i c a t e t h a t m o s t o f t h e p h e n o t y p i cv a r i a ti o n s e e n b y t h e b r e e d e r i n s e g r e g a t i n g p o p u l a -t i o n s in t h e ea r l y g en e ra t i o n s o f th e p ed i g re e i sen v i ro n men t a l i n o r i g i n , r a t h e r t h an g en e t i c , s o t h a ti n a t t emp t i n g t o p r ac t i ce s e l ec t i o n fo r y i e l d , t h eb r e e d e r m u s t b e d o i n g l i t t l e m o r e t h a n c h o o s i n gp l a n t s o r f a m i l i e s t h a t h a v e e n j o y e d a f a v o u r a b l ee n v i r o n m e n t . T h e e m p i r i c a l e v i d e n c e i s c o n s i s t e n tw i t h t h e t h eo ry s i n ce , a s men t i o n ed ea r l i e r , Fah i m e ta l . ( 1 9 9 8 ) fo u n d t h a t n o n e o f th e F6 l i n e s p ro d u cedb y t h e p e d i g r e e m e t h o d h a d a s i g n i f i c a n t l y h i g h e ry i e l d t h an t h e b e s t l i n e s p ro d u ced b y s i n g l e s eedd es cen t i n e i t h e r c ro s s . T h e co n c l u s i o n h e re i s o b v i -o u s , n ame l y , t h a t i t i s b e t t e r t o d e f e r s e l ec t i o n w i t h i np ed i g ree s u n t i l t h e F6 g en e ra t i o n w h en p l an t s a r ee f f e c t i v e l y h o m o z y g o u s f o r g e n e s c o n t r o l li n g c h a r a c -t e r s o f i n t e r e s t , s o t h a t t h e i r f ami l y mean s p ro v i d e ar e l i ab l e g u i d e t o t h e i r g en e t i c mer i t . W h ere , h o w -ev e r , b r eed e r s n eed t o ca r ry o u t s e l ec t i o n fo r aq u a l i t a t i v e ch a rac t e r , s u ch a s r e s i s t an ce t o a p a r t i cu -l a r d i s ea s e o r p e s t , t h a t i s k n o w n t o b e co n t ro l l ed b ya s i n g l e ma j o r g en e , s e l ec t i o n co u l d b e ca r r i ed o u t o nF 2 i n d i v i d u a l s i n t h e n u r s e ry , p ro v i d e d t h a t b o t h t h ee x p r e s s i v i t y a n d p e n e t r a n c e o f t he g e n e i s k n o w n t ob e co m p l e t e , an d t h a t t h e s c r een i n g o f t h e s e i n d i v id -u a l s i s s u f f i c i en t l y t h o ro u g h t o e l i mi n a t e e s cap es . I nt h e s e s p ec i a l c i r cu ms t an ces , s i n g l e s eed d es cen t co u l db e i n i t i a t ed f ro m F 2 i n d i v i d u a l s k n o w n t o h a v e t h ed es i r ed p ro p e r t i e s .

Seco n d , w i t h t h e n ew p ro ced u re , a l l q u an t i t a t i v ech a rac t e r s a r e meas u red d i r ec t l y , y i e l d , f o r ex amp l e ,b e i n g s c o r e d a s t h e t o t a l w e i g h t o f g r a in p r o d u c e d b yt h e p l an t s o f e ach p l o t i n t h e t r i a l . W i t h t h e p ed i g reeme t h o d , o n t h e o t h e r h an d , t h e u s u a l p r ac t i c e i s t oa s s e s s ch a rac t e r s i n d i r ec t l y b y ey e i n t h e ea r l y g en e r -a t i o n s o f p ed i g ree s a t l e a s t . A p a r t f r o m t h e f ac t t h a ts co r i n g b y ey e i n t ro d u ces a f u r t h e r s o u rce o f e r ro r , inad d i t i o n t o t h a t c au s ed b y u n co n t ro l l ab l e en v i ro n -men t a l v a r i a t i o n , c au s i n g t h e h e r i t ab i l i t y o f a ch a rac -


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2 8 0 M.J. Lawrence, D. Senadhira / Field Crops Research 55 (1998) 275-281

t e r t o b e l o w e r t h a n i f t h e c h a r a c t e r h a d b e e n m e a -s u red , i t h a s l o n g b een k n o w n o n t h eo re t i c a l g ro u n d st h a t i n d i r ec t s e l ec t i o n i s ex p ec t ed t o g i v e a b e t t e rr e s p o n s e t h an d i r ec t s e l ec t i o n o n a ch a rac t e r o n l y i nr a t h e r s p ec i a l c i r cu ms t an ces , w h i ch a r e u n l i k e l y t ob e e n c o u n t e r e d i n p r a c t i c e ( F a l c o n e r a n d M a c k a y ,1 9 9 6 ; Fah i m e t a l . , 1 9 9 8 ) . T h e co n c l u s i o n h e re i sag a i n o b v i o u s , n ame l y , t h a t ch a rac t e r s o f i n t e r e s ts h o u l d b e a s s e s s ed d i r ec t l y , r a t h e r t h an i n d i r ec t l y ,a n d t h a t th e y s h o u l d b e m e a s u r e d , r a t h e r t h a n s c o r e db y e y e .

T h i rd , w i t h t h e n ew p ro ced u re , a l l d ec i s i o n s a r eb a s e d o n t h e p e r f o r m a n c e o f p l a n t s r a is e d i n a p p r o -p r i a t e l y r ep l i ca t ed an d r an d o mi s ed t r i a l s , s o t h a t i t i sp o s s i b l e t o d e t e r m i n e w h e t h e r d i f f e r e n c e s b e t w e e nf a m i l i e s a r e o f a m a g n i t u d e t h a t c a n b e a s c r i b e d t os amp l i n g v a r i a t i o n , o r w h e t h e r , a l t e rn a t i v e l y , t h e s ea r e s u f f i c i en t l y l a rg e a s t o i n d i ca t e t h a t t h ey d i f f e rg e n e t i c a l l y . W i t h t h e p e d i g r e e m e t h o d , h o w e v e r ,f ami l y p l o t s a r e n e i t h e r r ep l i ca t ed , n o r r an d o mi s edo v e r t h e a r ea o ccu p i ed b y t h e t r i a l . I n t h e s e c i r cu m-s t a n c e s , d i f f e r e n c e s b e t w e e n p l o t s c a u s e d b y t h ee n v i r o n m e n t a r e c o m p l e t e l y c o n f o u n d e d w i t h t h o s ec a u s e d b y g e n e t i c a l d i f f e r e n c e s b e t w e e n t h e m , m a k -i n g t h e r eco g n i t i o n o f t h e i r g en e t i c mer i t d i f f i cu l t , t os ay t h e l e a st . F i s h e r ( 1 9 2 5 , 1 9 3 5 ) f i rs t d r ew a t t en t i o nt o t h e c r u c ia l i m p o r t a n c e o f r e p l i c a ti o n a n d r a n d o m i -s a t i o n i n ex p e r i me n t s , a s a r e s u l t o f h i s an a l y s i s o fd a t a f r o m l o n g - t e r m f i e l d t r i a l s a t t h e R o t h a m s t e dA g r i cu l t u r a l Res ea rch S t a t i o n ; i t i s s u rp r i s i n g , t h e r e -fo r e , t h a t i t s h o u l d , ap p a ren t l y , s t i l l b e n eces s a ry t oe m p h a s i s e t h e i r i m p o r t a n c e s o m e 7 0 y e a r s l a t e r .

B e c a u s e c h a r a c t e r s a r e m e a s u r e d , r a t h e r t h a n a s -s e s s e d b y e y e , t h e n e w p r o c e d u r e d i f f e r s f r o m c o n -v en t i o n a l me t h o d s i n o n e fu r t h e r r e s p ec t : i t en t a i l st h e p ro ces s i n g an d s t a t i s t i c a l an a l y s i s o f a co n s i d e r -ab l e amo u n t o f n u mer i ca l d a t a . I n t h e p a s t , t h i sr e q u i r e m e n t c o u l d h a v e l i m i t e d t h e n u m b e r o f c h a r -ac t e r s t h a t b r eed e r s co u l d h an d l e . T h e p r e s en tw i d e s p r e a d a v a i l a b i l i t y o f p e r s o n a l c o m p u t e r s a n ds t a t i s t i c a l s o f t w a re , h o w ev e r , n o w mak es t h i s t a s ks t r a i g h t fo rw ard .

T h e re a r e t h r ee fu r t h e r p o i n t s w o r t h r a i s i n g ab o u tt h i s p ro ced u re , t h e f i r s t o f w h i ch co n ce rn s t h e t a s k o fev a l u a t i n g F6 f ami l i e s w i t h r e s p ec t t o a l l ch a rac t e r so f i n t e r e s t . I t w as p o i n t ed o u t e a r l i e r t h a t t h e p ro b a -b i l i t y o f ex t r ac t i n g a l i n e f ro m a c ro s s t h a t a ch i ev est h e t a rg e t s f o r a l l ch a rac t e r s s i mu l t an eo u s l y i s l i k e l y

t o b e v e r y l o w u n l e s s t h e n u m b e r o f c o m p o n e n t s o ft h e d e s i r ed ag g reg a t e p h en o t y p e i s s ma l l , o r t h eg e n e t i c c o r r e l a t i o n s b e t w e e n t h e s e c o m p o n e n t s a r eu n u s u a l l y f a v o u r a b l e . T h e s i m p l e c a l c u l a t i o n o nw h i ch t h i s co n c l u s i o n w as b a s ed , h o w ev e r , t a c i t l ya s s u m e d t h a t al l c o m p o n e n t s o f t h e a g g r e g a t e p h e n o -t y p e w e re o f eq u a l i m p o r t an ce . T h i s i s u n l ik e l y t o b et h e ca s e i n p r ac t i ce ; y i e l d , f o r ex amp l e , w i l l a l mo s ta l w a y s b e r e g a r d e d a s m o r e i m p o r t a n t t h a n o t h e rco mp o n en t s . I t i s , o f co u r s e , p o s s i b l e t o co n s i d e r t h a ts o m e c o m p o n e n t s a r e m o r e i m p o r t a n t t h a n o t h e r sw h e n m a k i n g ju d g e m e n t s a b o u t t h e v a lu e o f l in e s , a sw a s d o n e s u b j e c t i v e l y b y F a h i m e t a l . (1 9 9 8 ) w h e nev a l u a t i n g t h e i r F 6 f ami l i e s . T h i s t a s k co u l d b e ca r -r i e d o u t m o r e e f f i c i e n t l y , h o w e v e r , b y c o m p u t i n g a ni n d e x t h a t r e c o g n i s e d n o t o n l y t h a t t h e c o m p o n e n t so f t h e d e s i r e d a g g r e g a t e p h e n o t y p e a r e g e n e t i c a l l yc o r r e l a t e d , b u t a l s o t h a t s o m e a r e m o r e i m p o r t a n tt h an o t h e r s . T h e co n s t ru c t i o n o f s e l ec t i o n i n d i ce s i ss u m m a r i s e d b y F a l c o n e r a n d M a c k a y ( 1 9 96 ) , r e -v i e w e d b y L a w r e n c e ( 1 9 8 1 ) a n d t h e i r a p p l i c a t i o n t op l a n t b r e e d i n g b y B a k e r ( 1 9 8 6 ) . T h e u s e o f i n d i c e si n ev a l u a t i n g an d r an k i n g F 6 f ami l i e s w o u l d p u t t h i st a s k o n t h e s a m e o b j e c t i v e a n d s y s t e m a t i c b a s i s a st h e a s s e s s m en t o f c ro s s e s a t t h e F 1 an d F 3 s t ag es o ft h e p ro ced u re .

Seco n d , a l t h o u g h t h e F 3 an d F6 s t ag es o f t h i sp r o c e d u r e h a v e b e e n t e s t e d o n a s m a l l s c a l e a g a i n s tt h r e e c o n v e n t i o n a l m e t h o d s w i t h t w o c r o s s e s , w h i c hs h o w ed i t t o b e a t l e a s t a s e f f ec t i v e a s t h e b e s t o f th el a t t e r a t a co n s i d e rab l y l o w er co s t (Fah i m e t a l . ,1 9 9 8 ) i n a s i n g l e s ea s o n i n S r i L an k a , i t w o u l d , o fco u r s e , b e d e s i r ab l e t o ca r ry o u t l a rg e r s ca l e t e s t si n v o l v i n g mo re c ro s s e s , r a i s ed i n d i f f e r en t s ea s o n s a td i f f e r en t s i t e s i n t h e l o w l an d t r o p i c s , i n o rd e r t od emo n s t r a t e t h a t i t s t h eo re t i c a l s u p e r i o r i t y o v e r t h ep e d i g r e e m e t h o d w a s c o n s i s t e n t l y r e a l i s e d i n p r a c -t i ce .

L a s t l y , a l t h o u g h t h i s n e w b r e e d i n g m e t h o d h a sb e e n d e v e l o p e d i n th e c o n t e x t o f s o l v in g a p a r t i c u la rp ro b l em w i t h r i c e , i t i s , o f co u r s e ap p l i cab l e t o an yc r o p p l a n t s p e c i e s w h e r e t h e e n d p r o d u c t s o f ab r e e d i n g p r o g r a m m e a r e in b r e d l in e s .

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B o c a R a t o n , F L .


7/7

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J i n k s , J . L ., P o o n i , H . S . , 1 9 76 . P r e d i c t i n g th e p r o p e r t i e s o f r e c o m -b i n a n t i n b r e d l i n e s d e r i v e d b y s i n g l e s e e d d e s c e n t . H e r e d i t y3 6 , 2 5 3 - 2 6 6 .

J i n k s , J .L . , P o o n i , H . S . , 1 9 8 0 . C o m p a r i n g p r e d i c t i o n s o f m e a np e r f o r m a n c e a n d e n v i r o n m e n t a l s e n s i t i v i t y o f r e c o m b i n a n t i n -b r e d l i n e s b a s e d u p o n F 3 a n d t r i p le t e s t c r o s s f a m i l i e s . H e r e d -i t y 4 5 , 3 0 5 - 3 1 2 .

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Perera , A .L .T . , 1985 . B iom et r i ca l s t ud i es i n r ice (Oryza sativa).P h D t h e s i s , U n i v . o f B i r m i n g h a m .

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