Rice is a staple food of the people in the world


Rice is a staple nutrient for most of the people in the universe. With the increasing of the universe population, Rice output is still a hot subject in rice genteelness despite of the increasing grain output after green revolution. Grain weight ( GW ) , grain figure per panicle ( GPP ) and panicle figure per works are thought to be three constituents of it. However, GW and GPP were frequently focused in the past QTL function surveies due to their high heritability. Of them, Numerous QTLs were located in last decennaries ( hypertext transfer protocol: //www.gramene.org/qtl/index.html ) . Some major QTLs of them were all right mapped and cloned in last several old ages. For cases, GS3, GW2, and qSW5/GW5 were cloned on the footing of QTL function ( Fan et al. , 2006 ; Song et al. , 2007 ; Shomura et al. , 2008 ; Weng et al. , 2008 ) . Gn1a, for GPP, was besides isolated by map-based cloning scheme ( Ashikari et al. , 2005 ) . Recently, Huang et Al. ( 2009 ) reported DEP1 conducts non merely vertical panicle but besides grain figure per panicle. On the other manus, Plant tallness ( PH ) and heading day of the month ( HD ) were the two traits, which indirectly affect rice grain output. The semidwarf cistron sd1 conveying the first green revolution of grain output ( Spielmeyer et al. , 2002 ) . Kojima et Al. ( 2002 ) found the cardinal HD cistron Hd3a that promotes blooming in rice. Besides, it was late reported that Ghd7 has effects non merely on HD and PH but besides on rice output ( Xue et al. , 2008 ) . Up to day of the month, the above major QTLs were isolated and cloned one after another. In add-on, a few output QTLs were all right mapped, such as gw8.1 and gw9.1 ( Xie et al. , 2006, 2008 ) , GPP1, gpa7 and SPP3b/TGW3b ( Liu et al. , 2009 ; Tian et al. , 2006 Liu et al. , 2009 ) , and so on. However, they did non wholly explicate the overall discrepancy of phenotype in rice. Hence, it is necessary and possible to observe a few new output or output associated character QTLs/genes which might be covered by the complex familial background.

It is of import to build a population for QTL function. A assortment of populations were used for mapping in past old ages, such as, F2, DH, RIL and BC populations. However, most research workers prefer to utilize RILs populations for mapping QTLs owing to its repeat in temporal and spacial. Up to day of the month, a larger figure of QTLs for grain output constituents were mapped utilizing RILs. However, it was used to build populations that derived from traversing between japonica and indica in past surveies, in which most major QTLs were easy identified. However, some rice assortments among intraspecies besides showed singular difference in grain size/shape and/or grain figure, such as two indica arable rice, Nanyangzhan with a bigger size grain and less grains per panicle, but Chuan7 with the opposite 1s. Hence, in position of restriction of traditional crossing combinations ( japonicaA-indica ) , it is possible to research more QTLs utilizing the population that derived from traversing between japonica and japonica or indica and indica, particularly there are some large difference between them in either familial background or/and phenotype. To our present cognition, it is advantageous to build a function population utilizing two parents which display a much more polymorphism in genome. Therefore, more QTLs and/or cistrons were likely to be discovered imputing to diverse allelomorphs between the parents genome. Hence, it is necessary and executable to develop some characteristic population in the procedure of QTL function. In this survey, a RIL population derived from a cross between two rice cultivars, Nanyangzhan and Chuan7, were used ( 1 ) to observe QTL for PH, HD, SPP and GW, ( 2 ) to measure the power of QTL sensing for output constituents as compared with other studies, ( 3 ) to place some QTL hot spots for all right function and cloning in farther survey.

Materials and methods

Maping population and field experiment

Maping populations consist of 185 recombinant inbred lines ( RILs ) derived from a cross between two indica rice Nanyangzhan and Chuan7 by single-seed descent. The 1000-grain weight is 43.3g in Nanyangzhan but 11.4g in Chuan7. The RIL F7 and F8 were planted in a bird-net-equipped field of the experimental farm of Huazhong Agricultural University in 2006 and 2007 rice turning seasons in Wuhan, China. Field tests were carried out following the randomised complete block design with two reproductions within each twelvemonth. One month subsequently from seeding, 10 seedlings of each line were transplanted into one row in the chief field and arranged in a 16.5 centimeter A- 26.4 centimeter lattice design. 8 workss in the center of each row were harvested separately to hit the traits.

Trait measuring

The HD was determined from the day of the month of seeding seed to first panicle outgrowth of works. After 20 yearss of complete header, PH was taken utilizing a long swayer from underside to the highest panicle of each works, separately. The workss were separately harvested, whose panicles were packed in little nylon cyberspace bags, and dried in the sunshine for one month and collected the phenotype informations for panicle figure, grain figure and grain weight. The Electronic Weighing machine was used to take the grain weight while the panicle figure, grain figure and no filling spine were counted by workers manually.

Deoxyribonucleic acid shapers and linkage map building

Fresh foliages of 185 lines in RIL ( F7 ) were collected separately for DNA extraction. Deoxyribonucleic acid was extracted utilizing a micro-isolation method as described by Cho et Al. ( 1996 ) with minor alterations. Polymorphous markers between the parents Nanyangzhan and Chuan7 were used for genotyping the population and the familial linkage map was constructed by utilizing MAPMAKER/EXP version 3.0b ( Lander et al. , 1987 ) .

QTL analysis in RILs was carried out utilizing composite interval function ( CIM ) performed by the computing machine plan Windows QTL cartographer 2.5 ( Wang et al. , 2007 ) . Window size was set at 10 centimeter, stepwise arrested development analysis was used to observe cofactors. QTL chief effects were estimated utilizing the maximum-likelihood appraisal method. LOD threshold at the experiment-wise significance degree of 0.05 was determined by calculating 1, 000 substitutions of each morphological character, and the LOD threshold ranged from 2.9-3.3. Heritability for the traits GL, GW and GT was calculated based on the experiments


Phenotypic fluctuation of the RIL population

A extremely important difference was observed in three of 5 investigated traits except for PH and output between the two parents Nanyangzhan and Chuan7 ( Table Nanyangzhan has a typical big grain size of over 43.3g per 1000 grains and little panicle of 91 spines per panicle with an earlier header day of the month. On the contrary, Chuan7 is a assortment with highly little grain size of 11.4g per 1000 grains and large panicle of 208 spines per panicle with a late header day of the month ; whereas, there were small difference in works tallness and output between them. However, fluctuation scope of PH in RILs population was from 63.0 to 189.0 and 84.1 to 170.4 in 2006 and 2007, severally. The similar state of affairs was happened in output. Meanwhile, taking two old ages data into consideration, 4 of five traits exhibited wide distribution in the RILs. Particularly, the upper limit of SPP was 3 times more than its lower limit in both old ages. Furthermore, output has the vastest discrepancy in the population, the border between upper limit and lower limit of it was more than 27g was observed. In add-on, the agencies of TGW in the RILs were 20.0 and 18.9 in 2006 and 2007, severally. On the other manus, transgressive segregation was observed for HD, PH, SPP and output except TGW ( Table 1 ) .

Heritability and correlativity

HD, PH, SPP and TGW showed higher wide heritability ranged from 79.4 % to 90.0 % , whereas the heritability of output was merely 33.5 % ( Table 1 ) . PH was extremely important positive correlativity with TGW and yield in two old ages ; nevertheless, the TGW, SPP and output were negative correlativity with HD, severally. Furthermore, SPP and TGW were positive correlativity with output, but a negative correlativity was detected between SPP and TGW in 2006 and 2007 ( Table 3 ) .

Familial linkage map

The familial linkage map consisted of 164 of 262 polymorphous markers, which was obtained by testing a sum of 502 SSR markers between the parents Nanyangzhan and Chuan7. 1635.9 cM genome part was harbored by this familial linkage map and its mean distance between next markers was of 9.9 centimeter ( Figure 1 ) .

QTL analysis for four traits

Heading day of the month

Wholly, four HD QTLs were located on chromosome 3, 5, 6, and 11, severally. Of them, qhd3 and qhd6 were detected repeatedly between 2006 and 2007. In add-on, qhd5 and qhd11were identified for one twelvemonth in 2007 and 2006, severally. On the other manus, LOD tonss and explained phenotypic discrepancy values of four QTLs ranged from 3.7 to 11.2 and 7.6 % to 27.7 % , severally. qhd6 was one of the major QTL for HD explicating up to 27 % phenotype discrepancy, Chuan7 allele with an increasing trait value. On the contrary, qhd5 and qhd11 showed an increasing consequence for HD by Nanyangzhan allelomorph

Plant tallness

A sum of four PH QTLs were identified in this function population. Two major QTLs, , qph1 and qph8, were detected in both old ages and located on chromosome 1 and 8, severally. Whereas, qph6 and qph12 were merely identified in 2006, and they have about the same linear consequence mark and explained about equal phonotype discrepancy. The LOD tonss of the two major QTLs were more than 10 and explained over 24 % of the phonotype discrepancy. Compared with them, qph6 and qph12 were two minor QTLs with LOD scores less than 4 and explained phonotype discrepancy below 6 % ( Table 2 ) .

Spines per panicle

Five SPP QTLs were identified in this survey on chromosome 3, 5, 7, 8 and 10, severally. In 2006, merely qspp5 was detected and Nanyangzhan allele increased the trait value. On the contrary, the other four QTLs, Chuan7 allele increased trait value, were merely detected in 2007. Among them, LOD tonss and explained phonotype discrepancy ranged from 3.0 to 5.3 and 6.6 % to 14.2 % , severally.

Thousand grain weight

Seven TGW QTLs were wholly detected in this QTL function. Of them, qtgw3a was a major QTL located on the kinetochore of chromosome 3 in both old ages. It ‘s LOD tonss was more than 15 and explained over 24 % of the phenotype discrepancy. In add-on, qtgw2, qtgw7 and qtgw9 were stably identified in two old ages, although their LOD tonss was less than 6.0 and explained below 11.0 % of the phenotype discrepancy. On the other manus, qtgw3b, qtgw5 and qtgw8, whose LOD tonss and explained phonotype discrepancy ranged from 3.9 to 6.8 and 6.0 to 12.6, severally, were merely identified in 2007. For all the QTLs detected here, Nanyangzhan allele positively affected the trait value.


QTL sensing does non depend wholly on the size of its consequence

A sum of 20 QTLs were identified in this survey. Of them, 8 QTLs were normally detected in both old ages. Additional three QTLs could besides be detected in two old ages if the LOD threshold decreased to 2.0 ( empirical threshold in rice ( Vanooijen 1999 ) ) . To our noticeable, the major QTL for the three traits were repeatedly detected in both old ages. Besides, some of minor TGW QTLs, Such as qtgw7 and qtgw9, were besides identified in both old ages, they might be chiefly conducted by grain length or/and breadth which are the high wide heritability traits. To our surprised, 4 minor QTLs for output were besides repeatedly observed with a LOD mark ranged from 0.7 to 1.8 ( informations non shown ) in both old ages. Their venue were overlapped with the qph1, qtgw5, qph8 and qtgw9, severally. It suggested that these venues have an consequence in output. In contrast, some QTLs were merely identified in individual twelvemonth, such as qhd5, qph6, qspp10 and so on. Especially, qtgw5, one of the major TGW QTL, was detected in this survey merely in 2007, which was perchance affected by the difference of make fulling rate in grain development procedure.

Powerful QTL sensing compared with old surveies

In all, six of 20 QTLs were foremost detected in this survey ( Table 2 ) , despite most QTLs overlapped with those of several studies in past. The major HD QTL, qhd6, was at the same place with Hd3a mapped by Monna et Al. ( 2002 ) . In the part of RM3513-RM347 on the long arm terminal of chromosome 3, qhd3 was matching to the venue of Hd6 mapped by Yamamoto et Al. ( 2000 ) and cloned by Takahashi et Al. ( 2001 ) . It was besides reported that Hd6 was involved in photoperiod sensitiveness and encodes a ? fractional monetary unit of protein kinase CK2. In the photoperiodic tract of rice blossoming, particularly, Hd3a play an of import function in passage from vegetive stage to reproductive stage ( Tamaki et al. , 2007 ) . They were easy detected in different populations, as their conservative maps in rice blossoming were easy affected by any mutant happened in rice genome development procedure. On the other manus, interestingly, qhd5 and qhd11 were detected in this population, but they were non found by Yano et Al. ( 2001 ) utilizing the combination of Nipponbare ( japonica ) and Kasalath ( indica ) where 14 HD QTLs were identified. However, qhd5 ( RM509-RM430 ) was like to be qDTH-5 detected from a BC2F2 population ( Milyang 23/O. rufipogon//Milyang 23 ) ( Cho et al. , 2003 ) . Besides, another similar population was developed and identified dth11.1 in the part RM167-RM209, where was near to the qhd11 ( RM209-RM229 ) detected in this survey ( Septiningsih et al. , 2003 ) . To our noticeable, one of the parentsused for mappingqDTH-5 and dth11.1 was wild rice. Hence, it is an evident attack to place some specific QTLs utilizing the population derived from a cross between cultivar rice and wild rice. Besides, qph1 was detected on the long arm terminal of chromosome 1 where was really near to the sd1 venue ( Monna et al. , 2002 ; Spielmeyer et al. , 2002 ) . It was besides identified for many times in different primary function populations ( Cho et al. , 1994 ; Huang et al. , 1996 ; Zhuang et al. , 1997 ; Xiao et al. , 1998 ; Moncada et al. , 2001 and Thomson et al. , 2003 ) . qph6 and qph12 were similar to cl6 and cl12 reported by Rahman et Al. ( 2007 ) , severally. However, qph8 was foremost detected in this population, which had a about tantamount consequence with qph1. It was reconfirmed that the characteristic populations were dearly-won proposed to mapping more new QTLs. In add-on, qtgw3a and qtgw5 were besides often identified by old research workers in different populations ( Ma et al. , 2004 ; Xing et al. , 2002 ; Cui et al. , 2003 ; Lin and Wu 2003 ; Thomson et al. , 2003 ) . The LOD mark of qtgw5 was 6.8 merely less than that of qtgw3a and explained up to 12.6 % discrepancy of phonotype, although it was merely detected in individual twelvemonth 2007. These two QTLs were the same venue of GS3 and GW5 which were the of import cistron for grain length and grain breadth in rice, severally. Particularly, it was reported that grain length in different assortments could be classed into two groups by a SNP in GS3 ( Fan et al. , 2009 ) . That is why qtgw3a was easy identified in most populations which derived from two parents with a different apparent grain size. Taken above together into consideration, it finally concluded that one population ca n’t map the whole QTLs in rice and different populations have different advantages. Therefore, the character population was needed to suggest for mapping extra QTL in future.

Correlation analysis among output and PH and HD

It is acceptable that PH has a positive correlativity with output and its some constituent factors, as each portion of the works is in proportion to turn up. A positive correlativity was observed between PH and output, TGW and SPP in this survey. On the other manus, a negative correlativity was detected in two old ages between the three traits and HD, severally. The similar consequences were besides reported by Rahman et Al. ( 2007 ) . It suggested that there is plenty more clip for sink variety meats to originate and develop by shortening vegetive stage. In contrast, two pleiotropic QTLs were late reported, which normally positively controlled PH and panicle size or output, but give rise to a late header at the same time ( Zhang et al. , 2006 ; Xue et al. , 2008 ) . To our noticeable, the two major HD QTLs identified in this survey were likely Hd3a and Hd6, severally. It is reported that they affect HD in different twenty-four hours length status, whereas no any output information was mentioned in those reported ( Monna et al. , 2002 ; Takahashi et al. , 2001 ) . However, harmonizing to present consequences, it is implied that these two QTLs likely indirectly map in rice output to some extent.

Familial dissection of the QTL bunchs

In contrast to qph1, the other major PH QTL, qph8, located on long arm terminal of chromosome 8, whose allelomorph from Nanyangzhan increased the phenotype value. Interestingly, the linear consequence mark of qph8 was closed to that of qph1 ( sd1 ) but opposite in linear way, moreover qph8 still explained more than 24.0 % of phenotype discrepancy though qph1 explained over 26.4 % ( Table 2 ) . On the other manus, there were two minor QTLs qspp8 and qtgw8 in the part between RM502 and RM264. It was seemingly questioned conditions qph8 has a major consequence on PH with a minor effects on SPP and TGW or three QTLs sharing near by venue. In old study, some QTLs showed a pleiotropic effects, such as cloned cistron GS3 which is a major cistron for grain length/weight with a minor consequence in grain breadth and thickness, and Ghd7 showed a pleiotropic effects in PH, HD, and SPP ( Fan et al. , 2006 ; Xue et al. , 2008 ) . In add-on, Zhang et Al. ( 2006 ) reported that one QTL was mapped to the short arm of chromosome 8 that conducted at the same time four traits ( SPP, GPP, HD and PH ) . In add-on, Xie et Al ( 2008 ) reported that a yield-enhancing QTL bunch was maped to 37.4Kb on chromosome 9, but whether more traits are controlled by individual cistron or different QTLs is still non clear. Interestingly, in the part RM22065-RM5720 where at that place besides were two QTLs, which were qtgw7 and qspp7 had been located at the same time on the same part. The NILs for these two new QTLs bunch had already been developed. The item consequences will be farther reported in hereafter.

In decision, fresh QTLs identified in this survey, particularly the two QTLs hot spot located severally on the long arm terminal of chromosome 7, 8 severally and a TWG QTL qtgw9 could be farther mulct mapped and cloned in future. Besides, the QTLs overlapped with old studies were once more located in the present survey could turn out their genuineness and dependableness. On the other manus, these consequences made a good familial footing to use characteristic allelomorphs for rice betterment by MAS genteelness.



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