基于水稻SSSLs的耐逆抗病基因（QTL）鉴定及育种利用
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摘要
本研究利用水稻两系骨干亲本,测序品种9311(籼稻)为受体亲本,日本晴(Nipponbare,粳稻)为供体亲本构建的92个单片段代换系(SSSLs),对水稻耐冷性、耐旱性、稻瘟病和稻曲病抗性进行了分析,并进行了耐(抗)逆基因(QTL)鉴定和育种利用研究,结果如下：
1、在芽期和苗期对SSSLs和亲本分别进行4℃和13℃/7℃(白天/晚上)低温处理,以处理后的芽期恢复成活率和苗期卷叶程度作为耐冷性评价指标。结果表明,日本晴芽期和苗期耐冷性极显著强于9311,不同SSSLs芽期和苗期耐冷性存在极显著差异,有4个代换系芽期耐冷性较强(SSR%>70.00%),6个代换系苗期耐冷性(NLR%>60.00%)较强,粳稻耐冷基因的导入增强了9311耐冷性。芽期和苗期耐冷性均较好的代换系X724和X733较好地保持了9311的农艺性状,产量等性状GCA优于9311,所配组合比对照增产2.58%-9.42%。鉴定出17个芽期耐冷QTL和5个苗期耐冷QTL,分布于12条染色体上的20个代换片段中,第12染色体的RM519和RM17区域同时检测出芽期和苗期耐冷QTL；芽期耐冷QTL qCTP9、qCTP11.2、 qCTP12.1和苗期耐冷QTL qCTS1.1、qCTSl.2具有较大加性效应,为主效耐冷QTL,对应代换系耐冷性较强。
2、利用田间直接鉴定法对SSSLs和亲本进行耐旱性鉴定,在干旱胁迫下,SSSLs及亲本的株高、穗粒数、有效穗、结实率、千粒重和单株产量显著下降,生育期显著延长,但不同SSSLs受影响程度不同。以结实率和单株产量作为耐旱性筛选指标,有25个SSSLs耐旱性强于受体亲本9311,耐旱株系X699、X705和X707综合农艺性状优良,且产量相关性状GCA优于对照,可作为耐旱亲本应用于耐旱两系杂交水稻选育。共检测出47个干旱条件下农艺性状QTL和31个与各性状耐旱性相关的QTL,分别定位于水稻12条染色体上的30个染色体区域。耐旱QTL qRPN4、qRPN5、 qRPN12.1qRSSR9和6个产量耐旱QTL为主效耐旱QTL位点。此外,第4染色体的RM16792-RM185区域,第5染色体RM421-RM31区域,第6染色体RM141区域,第9染色体RM410-RM201区域,第12染色体RM1261-RM519区域存在多个性状耐旱QTL,这些成蔟在同一区域的多个QTLs,可能是一因多效或紧密连锁的基因效应。
3、采用田间自然诱发鉴定的方法,在四川省稻瘟病和稻曲病常发区,对SSSLs和亲本进行抗病性鉴定。结果表明,供体亲本日本晴稻瘟病和稻曲病抗性均优于受体亲本9311。不同SSSL对稻瘟病和稻曲病的抗性不同,有3个代换系在两个鉴定点表现出较强的稻瘟病抗性,同一材料在两个试验点稻瘟病鉴定结果具有相对一致性(r=0.325**)。有7个代换系稻曲病抗性较强(病穗率均为0)。抗稻瘟病株系X565,抗稻曲病株系X723综合农艺性状优良,所配组合表现出较强的杂种优势,可作为优良的抗病杂交稻亲本用于抗病品种选育。以病穗率为抗性表型值,共检测出11个稻瘟病抗性QTL和8个稻曲病抗性QTL,分别位于除第6、10、11染色体外的9条染色体上。其中,稻瘟病抗性位点qBR1.3和qBR5同时在两个鉴定点被检测到,稳定性较强,加性效应较大,为主效QTL位点。稻曲病抗性QTL qFSR2与稻瘟病抗性QTL qBR2.1位同一代换系的相同代换片段中,且均为负效应位点,代换系同时具有较强的稻曲病和稻瘟病抗性增强,对应代换系稻瘟病和稻曲病病穗率分别为14.59%和0,比对照9311极显著降低,为多抗位点；qFSR9.1和qBR9也同时存在于同一代换系的同一代换片段中,但效应方向相反,代换系稻曲病病穗率较对照9311增加150.94%,稻瘟病病穗率降低89.32%。
In this research, we have generated92SSSLs using the two sequenced rice varieties (indica rice cultivar9311and japonica rice cultivar Nipponbare) as recurrent and donor parents, respectively. On this basis, cold tolerance and drought tolerance of rice, rice blast and false smut disease resistance were analyzed, and we identified several resistance genes (QTLs), and studied the application of those materials in rice breeding.The main results were as follows:
1. We treated SSSLs and parents in the condition of4℃and13℃/7℃(day/night) at plumule and seedling stages respectively, and took Survival Seedling Rate (SSR%) and Normal Leaves Rate (NLR%) as the indexes for cold tolerance evaluation. As a result, the cold tolerance of Nipponbare was highly significant better than9311at both plumule stage and seedling stage, and the cold tolerance of different SSSLs was significantly different. The SSSLs, including X709, X712, X686, and X729, had a strong cold tolerance at the plumule stage, and the SSR>70.00%. The SSSLs (X404, X634, X649, X732, X733, and X738) had a strong cold tolerance at seedling stage, and the NLR>60.00%. Therefore, the introgression of japonica segments into those SSSLs could enhance its cold tolerance. X724and X733, which had a superior cold tolerance at both plumule stage and seedling stage, maintained the9311elite agronomic traits, meanwhile, have higher GCA of yield trait than9311. In this research, we totally identified17QTLs with cold tolerance at the plumule stage, and5QTLs with cold tolerance at the seedling stage, which were located on20segments distributed on12chromosomes. Among these, we detected a cold tolerance QTL at plumule stages and seedling stages simultaneously between RM519and RM17on chromosomes12; the QTLs with cold tolerance at the plumule stage (qCTP9, qCTP11.2, qCTP12.1) and the QTLs with cold tolerance at the seedling stage (qCTS1.1and qCTS1.2) had a significant additive effect, and the corresponding substitution lines had a strong cold tolerance at9311background.
2. We evaluated the drought tolerance of the SSSLs and parents in field, and found that the plant height, grain number, effective panicle number, seed setting rate, grain weight and yield per plant of the SSSLs and parents were significantly decreased under the condition of drought stress, but the significantly differences for drought tolerance was found among different SSSLs. Taking the seed setting rate and yield per plant as drought tolerance evaluation indexes, we identified25SSSLs which had stronger drought tolerance than the parent9311. Among these, under the condition of drought stress, X705and X707had a>80%seed setting rate; the yield per plant of X633and X707reached more than14gram. Compared with normal irrigation, X707, X632, X630, X699and X666had a few yield losses under the condition of drought stress. Comparing to the CK9311, drought-resistant lines (X699, X705and X707) had elite agronomic performance and the GCA of yield-related traits, which could be used to breed drought-resistant hybrid rice.47QTLs related plant height, heading date, grain number, effective panicle number, seed setting rate and yield-related had been detected through t-test (P<0.001) between the SSSLs and recipient.31QTLs related drought tolerance were located at30regions on rice12chromosomes. Among these QTLs,13QTLs related plant height all had positive effects except qPH5.2and qRPH5,59QTLs related heading date, grain number, effective panicle number, seed setting rate and yield-related all had negative effect except for qDH10, qSN4, qRPN1.1, qRGY1. In addition, some segments contain multiple QTL loci affecting different traits, such as the region of RM16792-RM185on chromosome4, the region of RM421-RM31on chromosome5, the region of RM141on chromosome6, the region of RM410-RM201on chromosome9, the region of RM1261-RM519on chromosome12. These multiple QTLs in the same area, maybe have the pleiotropic effects or closely linked genes effect.
3. We evaluated the disease resistance of the SSSLs and parents using "natural field induced" identification methods for the rice blast and false smut in Sichuan Province. The results showed that both the rice blast and false smut resistance of the donor parent Nipponbare were better than the receptor9311. The rice blast and false smut resistance varied between different substitution lines,37lines had strong rice blast resistance at Ya'an point, and the average disease spike rate was from3.17%to17.50%. X648, X565and X646had strong rice blast resistance at Pujiang point, and the average disease spike rate was from8.89%to15.65%, the identification results of the same material had a relative consistency in two points (r=0.325**). Substitution lines X411, X560, X496, X495, X509, X704and X441had a strong false smut resistance (disease spike rates all were0). The different resistance genes derived from Nipponbare caused different disease resistance although the substitution lines had the same background. Blast-resistance line X565had excellent agronomic traits with moderate plant height and heading date, longer spike and more grains, grain weight higher, higher seed setting rate and higher yield than the CK9311, additionally, all the GCA of grain number, seed setting rate and yield were higher than that of9311. Blast-resistance lines X656, X437, X697, X671and X701had excellent agronomic traits, with moderate heading date and plant height (the X701slightly higher), strong tillering (PN>4), large grain density (SN>200), high seed setting rate (SSR>90%), large grain weight (TGW>30g), and yield was higher than9311; X679, X723, X704, X705, X701, X656and X717had a strong yield-related combining ability, which could be used as materials to breed blast-resistant hybrid rice. Taking the disease spike rate as the value of the resistance phenotype,11QTLs for rice blast resistance and8QTLs for false smut resistance were detected, which were located on6,9,10,11chromosomes. Among these,17QTLs had negative effects, which corresponding introgression segments enhanced the resistance of substitution lines, and2QTLs had positive effects, which introgression segments decreased the resistance of substitution lines. Blast-resistance locus qBR1.3and qBR5were detected at two points, additive effects were-11.15,-30.74,-8.53,-27.41, respectively. False smut resistance QTL qFSR2and rice blast resistance QTL qBR2.1were located at the same substitution segment of the same substitution line, and both QTLs had negative effects, the blast and false smut disease spikes rate of corresponding substitution line X560were14.59%and0respectively, and were significantly decreased comparing to9311, qFSR9.1and qBR9also existed at the same substitution segment of the same substitution line, but the effect was adverse, the additive effect was2.82and-13.25respectively. Compared with9311, the false smut disease spike rate of substitution lines was increased by150.94%, the rice blast disease spike rate of substitution lines was reduced by89.32%.
1、在芽期和苗期对SSSLs和亲本分别进行4℃和13℃/7℃(白天/晚上)低温处理,以处理后的芽期恢复成活率和苗期卷叶程度作为耐冷性评价指标。结果表明,日本晴芽期和苗期耐冷性极显著强于9311,不同SSSLs芽期和苗期耐冷性存在极显著差异,有4个代换系芽期耐冷性较强(SSR%>70.00%),6个代换系苗期耐冷性(NLR%>60.00%)较强,粳稻耐冷基因的导入增强了9311耐冷性。芽期和苗期耐冷性均较好的代换系X724和X733较好地保持了9311的农艺性状,产量等性状GCA优于9311,所配组合比对照增产2.58%-9.42%。鉴定出17个芽期耐冷QTL和5个苗期耐冷QTL,分布于12条染色体上的20个代换片段中,第12染色体的RM519和RM17区域同时检测出芽期和苗期耐冷QTL；芽期耐冷QTL qCTP9、qCTP11.2、 qCTP12.1和苗期耐冷QTL qCTS1.1、qCTSl.2具有较大加性效应,为主效耐冷QTL,对应代换系耐冷性较强。
2、利用田间直接鉴定法对SSSLs和亲本进行耐旱性鉴定,在干旱胁迫下,SSSLs及亲本的株高、穗粒数、有效穗、结实率、千粒重和单株产量显著下降,生育期显著延长,但不同SSSLs受影响程度不同。以结实率和单株产量作为耐旱性筛选指标,有25个SSSLs耐旱性强于受体亲本9311,耐旱株系X699、X705和X707综合农艺性状优良,且产量相关性状GCA优于对照,可作为耐旱亲本应用于耐旱两系杂交水稻选育。共检测出47个干旱条件下农艺性状QTL和31个与各性状耐旱性相关的QTL,分别定位于水稻12条染色体上的30个染色体区域。耐旱QTL qRPN4、qRPN5、 qRPN12.1qRSSR9和6个产量耐旱QTL为主效耐旱QTL位点。此外,第4染色体的RM16792-RM185区域,第5染色体RM421-RM31区域,第6染色体RM141区域,第9染色体RM410-RM201区域,第12染色体RM1261-RM519区域存在多个性状耐旱QTL,这些成蔟在同一区域的多个QTLs,可能是一因多效或紧密连锁的基因效应。
3、采用田间自然诱发鉴定的方法,在四川省稻瘟病和稻曲病常发区,对SSSLs和亲本进行抗病性鉴定。结果表明,供体亲本日本晴稻瘟病和稻曲病抗性均优于受体亲本9311。不同SSSL对稻瘟病和稻曲病的抗性不同,有3个代换系在两个鉴定点表现出较强的稻瘟病抗性,同一材料在两个试验点稻瘟病鉴定结果具有相对一致性(r=0.325**)。有7个代换系稻曲病抗性较强(病穗率均为0)。抗稻瘟病株系X565,抗稻曲病株系X723综合农艺性状优良,所配组合表现出较强的杂种优势,可作为优良的抗病杂交稻亲本用于抗病品种选育。以病穗率为抗性表型值,共检测出11个稻瘟病抗性QTL和8个稻曲病抗性QTL,分别位于除第6、10、11染色体外的9条染色体上。其中,稻瘟病抗性位点qBR1.3和qBR5同时在两个鉴定点被检测到,稳定性较强,加性效应较大,为主效QTL位点。稻曲病抗性QTL qFSR2与稻瘟病抗性QTL qBR2.1位同一代换系的相同代换片段中,且均为负效应位点,代换系同时具有较强的稻曲病和稻瘟病抗性增强,对应代换系稻瘟病和稻曲病病穗率分别为14.59%和0,比对照9311极显著降低,为多抗位点；qFSR9.1和qBR9也同时存在于同一代换系的同一代换片段中,但效应方向相反,代换系稻曲病病穗率较对照9311增加150.94%,稻瘟病病穗率降低89.32%。
In this research, we have generated92SSSLs using the two sequenced rice varieties (indica rice cultivar9311and japonica rice cultivar Nipponbare) as recurrent and donor parents, respectively. On this basis, cold tolerance and drought tolerance of rice, rice blast and false smut disease resistance were analyzed, and we identified several resistance genes (QTLs), and studied the application of those materials in rice breeding.The main results were as follows:
1. We treated SSSLs and parents in the condition of4℃and13℃/7℃(day/night) at plumule and seedling stages respectively, and took Survival Seedling Rate (SSR%) and Normal Leaves Rate (NLR%) as the indexes for cold tolerance evaluation. As a result, the cold tolerance of Nipponbare was highly significant better than9311at both plumule stage and seedling stage, and the cold tolerance of different SSSLs was significantly different. The SSSLs, including X709, X712, X686, and X729, had a strong cold tolerance at the plumule stage, and the SSR>70.00%. The SSSLs (X404, X634, X649, X732, X733, and X738) had a strong cold tolerance at seedling stage, and the NLR>60.00%. Therefore, the introgression of japonica segments into those SSSLs could enhance its cold tolerance. X724and X733, which had a superior cold tolerance at both plumule stage and seedling stage, maintained the9311elite agronomic traits, meanwhile, have higher GCA of yield trait than9311. In this research, we totally identified17QTLs with cold tolerance at the plumule stage, and5QTLs with cold tolerance at the seedling stage, which were located on20segments distributed on12chromosomes. Among these, we detected a cold tolerance QTL at plumule stages and seedling stages simultaneously between RM519and RM17on chromosomes12; the QTLs with cold tolerance at the plumule stage (qCTP9, qCTP11.2, qCTP12.1) and the QTLs with cold tolerance at the seedling stage (qCTS1.1and qCTS1.2) had a significant additive effect, and the corresponding substitution lines had a strong cold tolerance at9311background.
2. We evaluated the drought tolerance of the SSSLs and parents in field, and found that the plant height, grain number, effective panicle number, seed setting rate, grain weight and yield per plant of the SSSLs and parents were significantly decreased under the condition of drought stress, but the significantly differences for drought tolerance was found among different SSSLs. Taking the seed setting rate and yield per plant as drought tolerance evaluation indexes, we identified25SSSLs which had stronger drought tolerance than the parent9311. Among these, under the condition of drought stress, X705and X707had a>80%seed setting rate; the yield per plant of X633and X707reached more than14gram. Compared with normal irrigation, X707, X632, X630, X699and X666had a few yield losses under the condition of drought stress. Comparing to the CK9311, drought-resistant lines (X699, X705and X707) had elite agronomic performance and the GCA of yield-related traits, which could be used to breed drought-resistant hybrid rice.47QTLs related plant height, heading date, grain number, effective panicle number, seed setting rate and yield-related had been detected through t-test (P<0.001) between the SSSLs and recipient.31QTLs related drought tolerance were located at30regions on rice12chromosomes. Among these QTLs,13QTLs related plant height all had positive effects except qPH5.2and qRPH5,59QTLs related heading date, grain number, effective panicle number, seed setting rate and yield-related all had negative effect except for qDH10, qSN4, qRPN1.1, qRGY1. In addition, some segments contain multiple QTL loci affecting different traits, such as the region of RM16792-RM185on chromosome4, the region of RM421-RM31on chromosome5, the region of RM141on chromosome6, the region of RM410-RM201on chromosome9, the region of RM1261-RM519on chromosome12. These multiple QTLs in the same area, maybe have the pleiotropic effects or closely linked genes effect.
3. We evaluated the disease resistance of the SSSLs and parents using "natural field induced" identification methods for the rice blast and false smut in Sichuan Province. The results showed that both the rice blast and false smut resistance of the donor parent Nipponbare were better than the receptor9311. The rice blast and false smut resistance varied between different substitution lines,37lines had strong rice blast resistance at Ya'an point, and the average disease spike rate was from3.17%to17.50%. X648, X565and X646had strong rice blast resistance at Pujiang point, and the average disease spike rate was from8.89%to15.65%, the identification results of the same material had a relative consistency in two points (r=0.325**). Substitution lines X411, X560, X496, X495, X509, X704and X441had a strong false smut resistance (disease spike rates all were0). The different resistance genes derived from Nipponbare caused different disease resistance although the substitution lines had the same background. Blast-resistance line X565had excellent agronomic traits with moderate plant height and heading date, longer spike and more grains, grain weight higher, higher seed setting rate and higher yield than the CK9311, additionally, all the GCA of grain number, seed setting rate and yield were higher than that of9311. Blast-resistance lines X656, X437, X697, X671and X701had excellent agronomic traits, with moderate heading date and plant height (the X701slightly higher), strong tillering (PN>4), large grain density (SN>200), high seed setting rate (SSR>90%), large grain weight (TGW>30g), and yield was higher than9311; X679, X723, X704, X705, X701, X656and X717had a strong yield-related combining ability, which could be used as materials to breed blast-resistant hybrid rice. Taking the disease spike rate as the value of the resistance phenotype,11QTLs for rice blast resistance and8QTLs for false smut resistance were detected, which were located on6,9,10,11chromosomes. Among these,17QTLs had negative effects, which corresponding introgression segments enhanced the resistance of substitution lines, and2QTLs had positive effects, which introgression segments decreased the resistance of substitution lines. Blast-resistance locus qBR1.3and qBR5were detected at two points, additive effects were-11.15,-30.74,-8.53,-27.41, respectively. False smut resistance QTL qFSR2and rice blast resistance QTL qBR2.1were located at the same substitution segment of the same substitution line, and both QTLs had negative effects, the blast and false smut disease spikes rate of corresponding substitution line X560were14.59%and0respectively, and were significantly decreased comparing to9311, qFSR9.1and qBR9also existed at the same substitution segment of the same substitution line, but the effect was adverse, the additive effect was2.82and-13.25respectively. Compared with9311, the false smut disease spike rate of substitution lines was increased by150.94%, the rice blast disease spike rate of substitution lines was reduced by89.32%.
引文
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