陆地棉种子品质性状遗传及其QTL定位研究
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摘要
棉花是最重要的经济作物之一。棉花生产中纤维是主要的收获对象,而棉花种子是棉花生产的副产品。棉花种子的用途十分广泛,它是棉花生产的基本生产资料,也是重要的食用油和蛋白质资源。棉花种子品质性状的遗传及其QTL定位研究对于棉花种子品质的遗传改良具有重要的理论和实践意义。本研究选用49份不同蛋白质和棉酚含量的陆地棉种质资源和188份陆地棉重组近交系材料,以多年份、多地点种植收获的种子材料组成原始样品集,建立了近红外反射光谱(NIRS)定标模型,研究应用近红外反射光谱法测定棉仁粉蛋白质含量和棉酚含量的可行性；同时采用包括基因型和基因型×环境互作的双子叶植物二倍体种子数量性状遗传模型,按完全双列杂交设计,研究了陆地棉种子品质性状的遗传效应、遗传率、遗传相关性、遗传效应预测和杂种优势表现等。此外,以陆地棉品种间重组自交系为材料,采用随机交配技术,获得了188个系间交配的“永久F2”群体,并运用本实验室构建的该群体的分子连锁图谱,应用QTLNetwork 2.0软件对“永久F2”群体在两个环境下测得的种子品质性状进行QTL定位研究,确定单个基因的位置及效应。主要研究如下：
1.采用改进的偏最小二乘法(Modified PLS)和(2,4,4,1)的数学转换的方法建立了棉仁粉蛋白质和棉酚含量的近红外反射光谱(NIRS)定标模型。该定标模型的蛋白质含量定标决定系数(RSQ)为0.93和交叉检验决定系数(1-VR)为0.93,定标标准误差(SEC)和交互校验标准误差(SECV)分别为0.62和0.64,预测模型的建模效果优良,可替代化学分析。棉酚含量预测模型的RSQ、1-VR、SEC和SECV分别为0.84、0.81、0.07和0.08,模型预测效果略差于蛋白质模型,但仍可用于棉仁粉中棉酚含量的测定.
2.采用基因型和基因型×环境互作的二倍体种子数量性状遗传模型和统计分析方法,分析了陆地棉12个亲本及其双列杂交组合种子品质性状的遗传效应、遗传率和遗传相关,结果表明：
①遗传主效应和环境互作效应分析表明,种仁率、蛋白质含量和油分含量以遗传主效应为主,而籽指、仁指、仁壳比和棉酚含量则是以基因型×环境互作效应为主.所有研究的性状几乎都以母体植株遗传效应为主,其次为细胞质效应。四个种子物理性状均受环境影响大,其中籽指、仁指、仁壳比的母体植株遗传是以显性效应为主,种仁率以细胞质效应为主。蛋白质和油分含量以母体加性效应为主、母体植株普通遗传率较高,而棉酚含量以母体显性×环境互作效应以及细胞质效应为主,细胞质遗传率较高。
②棉花种子物理与营养品质性状间的相关性分析表明,籽指与蛋白质含量、油分含量间以胚加性相关为主,籽指与棉酚含量的相关受环境影响大,母体加性与环境互作负相关较为重要；仁指与三个营养品质性状的相关受环境影响较大,分别以胚显性互作负相关、胚加性互作正相关、细胞质和母体显性互作负相关为主；种仁率与蛋白质、油分和棉酚含量分别以母体加性正相关、母体加性负相关和细胞质负相关为主；仁壳比与三个营养品质性状分别以母体加性正相关、胚×环境互作正相关和细胞质负相关为主。营养品质性状间相关性分析结果表明,蛋白质含量与油分含量呈极显著的负相关；蛋白质与棉酚含量以胚显性负相关为主；油分含量与棉酚含量以极显著的胚显性正相关为主。因此,在棉花种子品质性状的改良中,可利用这些性状的相关进行性状间的间接选择。
③7个棉花种子品质性状存在着不同程度的杂种优势,但杂种优势的表现程度和方向存在着较大的差异,其中籽指、仁指和仁壳比以母体优势为主,种仁率以细胞质优势为主,蛋白质含量以母体优势为主,油分含量以胚优势和母体优势为主,棉酚含量以母体优势为主。籽指、仁指和种仁率还存在着较大的环境互作优势；仁壳比、蛋白质含量、油分含量和棉酚含量这几个性状的互作优势不明显,它们主要受遗传主效应杂种优势的影响。
④不同亲本在棉花种子品质性状的改良中具有特定的利用价值,其中SGK 3可以明显增加棉花种子的籽指；H 556可明显增加杂种后代的仁指；SGK 3、中棉所44、浙905、鲁2015和H 556会增加后代的种仁率；126系9、AY-4、浙1793、鲁2015和H 556能明显增加后代的仁壳比；AY-4、浙905和Z1138会增加杂种后代的蛋白质含量；126系9、浙1793、、R808、H 556和J 220在棉花高油分育种中具有较好的种用价值；而中棉所44、AY-4、浙905、R 808和鲁2015可以明显降低后代的棉酚含量。
3.创建了一套陆地棉品种间“永久F2”群体。选用陆地棉品种间杂交组合(HS46×MARCABUCAG8US-1-88) 188个近交系为材料,对其进行重组近交系间的随机交配,获得188个重组近交系系间交配的“永久F2”群体。采用本实验室构建的重组自交系分子连锁图谱,应用QTLNetwork 2.0软件对“永久F2”群体在两个环境下测得的种子品质性状进行QTL定位。共检测到17个与种子品质性状相关的主效QTLs和15对上位性QTLs,控制籽指的主效QTL和上位性位点各2个,共解释籽指性状总变异的.22.27%；控制仁指主效QTL2个和4对上位性位点,共解释仁指性状总变异的23.04%；控制种仁率的主效QTL4个和2对上位性位点,共解释种仁率性状总变异的19.70%；此外,本研究将控制仁壳比的主效QTL和上位性位点定位于第.15号染色体上。对棉花种子营养品质性状定位结果表明,共检测到与蛋白质含量相关的主效QTL3个和1对上位性位点,共解释总遗传变异的12.13%；与种子油分含量相关的QTL和上位性位点各3个,但受环境影响大；与棉酚含量相关的QTL 4个,上位性位点2对,能解释棉酚含量变异仅为2.42%。
Cotton (Gossypium spp.) is the most important fibre crop in the world. As a main by-product of cotton, cottonseed is an important source of edible oil and protein meals. Due to its important economic value, there was an increasing interest for cotton breeders in improving cottonseed quality. One of the most important aspects for cottonseed quality improvement is to understand its genetic mechanism and develop fast testing methods for seed quality. Thus, the aims of present study are (1)to investigate the feasibility of quality measuring method with near-infrared reflectance spectroscopy, using 49 upland cotton (Gossypium hirsutum L.) germplasms and 188 recombinant inbred lines (RILs), which were harvested from different cotton growing regions in different years; (2)to determine genetic effect, heritability, correlation, the exploitation of F2 heterosis of cottonseed quality traits through the genetic models of diploid plant seed quantitative traits and corresponding statistical approaches with two years data under two kinds of environment, using twelve transgenic upland cotton parents with a diallel mating design; (3)to construct an "immortalized F2" (IF2) population including 188 single crosses; and (4)to analyze the frequency of molecular marker loci in IF2 population, using a molecular map with 388 different markers. The main results were summarized as follows:
(1) Protein and gossypol NIRS calibration equations of cottonseed were obtained with modified partial least squares (MPLS) through analyzing the scanning data with ISI software. The multiple correlation coefficients (RSQ) and statistic 1-variance ratio (1-VR) for the protein content NIRS calibration in cottonseed kernels were 0.93 and 0.93, respectively, and its standard error of calibration (SEC) and standard error of cross validation (SECV) were 0.62 and 0.64, respectively. The results indicated that NIRS could be used as a substitute for chemical methods in determination of protein content in cottonseed kernels. Also, the RSQ, SEC,1-VR and SECV for gossypol content determination of NIRS were 0.84,0.81,0.07 and 0.08, respectively. It showed a good fitting with chemical method although it was weaker than that of protein content NIRS.
(2)The genetic effect, heritability and genetic correlation of cottonseed quality traits including seed index (SI), kernel index (KI), kernel percentage (KP), kernel/hull (K/H), protein content (PC), oil content (OC) and gossypol content (GC) in twelve parents and their diallel mating were analyzed through the genetic models of diploid seed quantitative traits. The results showed that
①KP, PC and OC were mainly affected by genetic effect, and SI, KI, K/H and GC were mainly controlled by genetic×environmental interaction effect. In addition, all seed quality traits in this experiment were mainly controlled by maternal effects, followed by cytoplasmic effects. Four physical traits including SI, KI and K/H were dominantly controlled by environment effects. For cottonseed nutrient quality traits, PC and OC were mainly controlled by maternal additive effects. And the total narrow-sense heritabilities for PC and OC were high. GC was controlled by maternal dominance×environment interaction and cytoplasmic effects and having a high cytoplasm heritability. The results may supply some useful information for the improvement of seed quality by the genetic and breeding method.
②The phenotypic correlation and genotypic correlation components for quality traits indicated that genetic main correlations and GE interaction correlations from different genetic systems including diploid embryo, cytoplasm and diploid maternal plant were mostly significant for the pairwise quality traits excepted for K/H. The relationship for SI and GC, KI and PC, KI and OC, KI and GC were influenced by the environment conditions. A negative correlation between PC and OC, PC and GC was observed. However, the correlation between OC and GC was positive. Therefore, some cottonseed quality traits could be indirectly improved by the selection based on other traits effectively.
③Heterosis including the general heterosis and the GE interaction heterosis could be detected in the cottonseed quality traits, but the performance and main effect varied with the traits. The most important general heterosis of SI, KI, K/H, PC, OC and GC were maternal heterosis, while KP was mainly affected by cytoplasmic heterosis. In addition, SI, KI and KP were also controlled by interaction heterosis, but the interaction heterosis was not important for K/H, PC, OC and GC.
④The predicted values of genetic effects for 12 parents were also analyzed in this study. It showed that testing parents could play different role in cottonseed quality improvement breeding. For example, SGK 3 and H 556 have the effect to increase SI and KI in these offsprings; SGK 3, ZMS 44, ZHE 905, LU 2015 and H 556 could increase KP significantly; 126XI 9, AY-4, ZHE 1793, LU 2015 and H 556 could increase K/H in the following progenies; AY-4, ZHE 905 and Z 1138 were better than other for increasing PC; 126XI 9, ZHE 1793, R 808, H 556 and J 220 were important in the improvement of OC in seeds; and ZMS 44, AY-4, ZHE 905、R 808 and LU 2015 were the good germplasm to decrease GC in cottonseeds.
(3) An "immortalized F2" (IF2) population including 188 single crosses was constructed by using a set of recombinant inbred line (RIL) derived from the hybrid of HS46×MARCABUCAG8US-1-88. With this IF2 population, the frequency of molecular marker loci, QTL mapping and effect of single loci for seed quality traits were analyzed using a molecular map with 388 markers by software of QTL Network. Seventeen main effects and fifteen epistasis in QTLs were identified for cottonseed quality traits including SI, KI, KP, K/H, PC, OC and GC. Two of main QTL and epistasis were found closely correlated with SI, and the total variation explained was 22.27%; And two main QTL and four epistasis attribute to KI, and explained 23.04% variation; and four main QTL and 2 epistasis could explain 19.70% total variation of KP. Further, present study located the main QTL of K/H in the 15 chromosome. Also, the number of closely related main QTL and epistasis for protein, oil, gossypol content are 3-1,3-3, and 4-2, respectively. And the variation explained are 2.42%～23.04%. These QTLs detected for seed quality traits in cotton are expected to be useful in the breeding program for cottonseed nutrient quality.
1.采用改进的偏最小二乘法(Modified PLS)和(2,4,4,1)的数学转换的方法建立了棉仁粉蛋白质和棉酚含量的近红外反射光谱(NIRS)定标模型。该定标模型的蛋白质含量定标决定系数(RSQ)为0.93和交叉检验决定系数(1-VR)为0.93,定标标准误差(SEC)和交互校验标准误差(SECV)分别为0.62和0.64,预测模型的建模效果优良,可替代化学分析。棉酚含量预测模型的RSQ、1-VR、SEC和SECV分别为0.84、0.81、0.07和0.08,模型预测效果略差于蛋白质模型,但仍可用于棉仁粉中棉酚含量的测定.
2.采用基因型和基因型×环境互作的二倍体种子数量性状遗传模型和统计分析方法,分析了陆地棉12个亲本及其双列杂交组合种子品质性状的遗传效应、遗传率和遗传相关,结果表明：
①遗传主效应和环境互作效应分析表明,种仁率、蛋白质含量和油分含量以遗传主效应为主,而籽指、仁指、仁壳比和棉酚含量则是以基因型×环境互作效应为主.所有研究的性状几乎都以母体植株遗传效应为主,其次为细胞质效应。四个种子物理性状均受环境影响大,其中籽指、仁指、仁壳比的母体植株遗传是以显性效应为主,种仁率以细胞质效应为主。蛋白质和油分含量以母体加性效应为主、母体植株普通遗传率较高,而棉酚含量以母体显性×环境互作效应以及细胞质效应为主,细胞质遗传率较高。
②棉花种子物理与营养品质性状间的相关性分析表明,籽指与蛋白质含量、油分含量间以胚加性相关为主,籽指与棉酚含量的相关受环境影响大,母体加性与环境互作负相关较为重要；仁指与三个营养品质性状的相关受环境影响较大,分别以胚显性互作负相关、胚加性互作正相关、细胞质和母体显性互作负相关为主；种仁率与蛋白质、油分和棉酚含量分别以母体加性正相关、母体加性负相关和细胞质负相关为主；仁壳比与三个营养品质性状分别以母体加性正相关、胚×环境互作正相关和细胞质负相关为主。营养品质性状间相关性分析结果表明,蛋白质含量与油分含量呈极显著的负相关；蛋白质与棉酚含量以胚显性负相关为主；油分含量与棉酚含量以极显著的胚显性正相关为主。因此,在棉花种子品质性状的改良中,可利用这些性状的相关进行性状间的间接选择。
③7个棉花种子品质性状存在着不同程度的杂种优势,但杂种优势的表现程度和方向存在着较大的差异,其中籽指、仁指和仁壳比以母体优势为主,种仁率以细胞质优势为主,蛋白质含量以母体优势为主,油分含量以胚优势和母体优势为主,棉酚含量以母体优势为主。籽指、仁指和种仁率还存在着较大的环境互作优势；仁壳比、蛋白质含量、油分含量和棉酚含量这几个性状的互作优势不明显,它们主要受遗传主效应杂种优势的影响。
④不同亲本在棉花种子品质性状的改良中具有特定的利用价值,其中SGK 3可以明显增加棉花种子的籽指；H 556可明显增加杂种后代的仁指；SGK 3、中棉所44、浙905、鲁2015和H 556会增加后代的种仁率；126系9、AY-4、浙1793、鲁2015和H 556能明显增加后代的仁壳比；AY-4、浙905和Z1138会增加杂种后代的蛋白质含量；126系9、浙1793、、R808、H 556和J 220在棉花高油分育种中具有较好的种用价值；而中棉所44、AY-4、浙905、R 808和鲁2015可以明显降低后代的棉酚含量。
3.创建了一套陆地棉品种间“永久F2”群体。选用陆地棉品种间杂交组合(HS46×MARCABUCAG8US-1-88) 188个近交系为材料,对其进行重组近交系间的随机交配,获得188个重组近交系系间交配的“永久F2”群体。采用本实验室构建的重组自交系分子连锁图谱,应用QTLNetwork 2.0软件对“永久F2”群体在两个环境下测得的种子品质性状进行QTL定位。共检测到17个与种子品质性状相关的主效QTLs和15对上位性QTLs,控制籽指的主效QTL和上位性位点各2个,共解释籽指性状总变异的.22.27%；控制仁指主效QTL2个和4对上位性位点,共解释仁指性状总变异的23.04%；控制种仁率的主效QTL4个和2对上位性位点,共解释种仁率性状总变异的19.70%；此外,本研究将控制仁壳比的主效QTL和上位性位点定位于第.15号染色体上。对棉花种子营养品质性状定位结果表明,共检测到与蛋白质含量相关的主效QTL3个和1对上位性位点,共解释总遗传变异的12.13%；与种子油分含量相关的QTL和上位性位点各3个,但受环境影响大；与棉酚含量相关的QTL 4个,上位性位点2对,能解释棉酚含量变异仅为2.42%。
Cotton (Gossypium spp.) is the most important fibre crop in the world. As a main by-product of cotton, cottonseed is an important source of edible oil and protein meals. Due to its important economic value, there was an increasing interest for cotton breeders in improving cottonseed quality. One of the most important aspects for cottonseed quality improvement is to understand its genetic mechanism and develop fast testing methods for seed quality. Thus, the aims of present study are (1)to investigate the feasibility of quality measuring method with near-infrared reflectance spectroscopy, using 49 upland cotton (Gossypium hirsutum L.) germplasms and 188 recombinant inbred lines (RILs), which were harvested from different cotton growing regions in different years; (2)to determine genetic effect, heritability, correlation, the exploitation of F2 heterosis of cottonseed quality traits through the genetic models of diploid plant seed quantitative traits and corresponding statistical approaches with two years data under two kinds of environment, using twelve transgenic upland cotton parents with a diallel mating design; (3)to construct an "immortalized F2" (IF2) population including 188 single crosses; and (4)to analyze the frequency of molecular marker loci in IF2 population, using a molecular map with 388 different markers. The main results were summarized as follows:
(1) Protein and gossypol NIRS calibration equations of cottonseed were obtained with modified partial least squares (MPLS) through analyzing the scanning data with ISI software. The multiple correlation coefficients (RSQ) and statistic 1-variance ratio (1-VR) for the protein content NIRS calibration in cottonseed kernels were 0.93 and 0.93, respectively, and its standard error of calibration (SEC) and standard error of cross validation (SECV) were 0.62 and 0.64, respectively. The results indicated that NIRS could be used as a substitute for chemical methods in determination of protein content in cottonseed kernels. Also, the RSQ, SEC,1-VR and SECV for gossypol content determination of NIRS were 0.84,0.81,0.07 and 0.08, respectively. It showed a good fitting with chemical method although it was weaker than that of protein content NIRS.
(2)The genetic effect, heritability and genetic correlation of cottonseed quality traits including seed index (SI), kernel index (KI), kernel percentage (KP), kernel/hull (K/H), protein content (PC), oil content (OC) and gossypol content (GC) in twelve parents and their diallel mating were analyzed through the genetic models of diploid seed quantitative traits. The results showed that
①KP, PC and OC were mainly affected by genetic effect, and SI, KI, K/H and GC were mainly controlled by genetic×environmental interaction effect. In addition, all seed quality traits in this experiment were mainly controlled by maternal effects, followed by cytoplasmic effects. Four physical traits including SI, KI and K/H were dominantly controlled by environment effects. For cottonseed nutrient quality traits, PC and OC were mainly controlled by maternal additive effects. And the total narrow-sense heritabilities for PC and OC were high. GC was controlled by maternal dominance×environment interaction and cytoplasmic effects and having a high cytoplasm heritability. The results may supply some useful information for the improvement of seed quality by the genetic and breeding method.
②The phenotypic correlation and genotypic correlation components for quality traits indicated that genetic main correlations and GE interaction correlations from different genetic systems including diploid embryo, cytoplasm and diploid maternal plant were mostly significant for the pairwise quality traits excepted for K/H. The relationship for SI and GC, KI and PC, KI and OC, KI and GC were influenced by the environment conditions. A negative correlation between PC and OC, PC and GC was observed. However, the correlation between OC and GC was positive. Therefore, some cottonseed quality traits could be indirectly improved by the selection based on other traits effectively.
③Heterosis including the general heterosis and the GE interaction heterosis could be detected in the cottonseed quality traits, but the performance and main effect varied with the traits. The most important general heterosis of SI, KI, K/H, PC, OC and GC were maternal heterosis, while KP was mainly affected by cytoplasmic heterosis. In addition, SI, KI and KP were also controlled by interaction heterosis, but the interaction heterosis was not important for K/H, PC, OC and GC.
④The predicted values of genetic effects for 12 parents were also analyzed in this study. It showed that testing parents could play different role in cottonseed quality improvement breeding. For example, SGK 3 and H 556 have the effect to increase SI and KI in these offsprings; SGK 3, ZMS 44, ZHE 905, LU 2015 and H 556 could increase KP significantly; 126XI 9, AY-4, ZHE 1793, LU 2015 and H 556 could increase K/H in the following progenies; AY-4, ZHE 905 and Z 1138 were better than other for increasing PC; 126XI 9, ZHE 1793, R 808, H 556 and J 220 were important in the improvement of OC in seeds; and ZMS 44, AY-4, ZHE 905、R 808 and LU 2015 were the good germplasm to decrease GC in cottonseeds.
(3) An "immortalized F2" (IF2) population including 188 single crosses was constructed by using a set of recombinant inbred line (RIL) derived from the hybrid of HS46×MARCABUCAG8US-1-88. With this IF2 population, the frequency of molecular marker loci, QTL mapping and effect of single loci for seed quality traits were analyzed using a molecular map with 388 markers by software of QTL Network. Seventeen main effects and fifteen epistasis in QTLs were identified for cottonseed quality traits including SI, KI, KP, K/H, PC, OC and GC. Two of main QTL and epistasis were found closely correlated with SI, and the total variation explained was 22.27%; And two main QTL and four epistasis attribute to KI, and explained 23.04% variation; and four main QTL and 2 epistasis could explain 19.70% total variation of KP. Further, present study located the main QTL of K/H in the 15 chromosome. Also, the number of closely related main QTL and epistasis for protein, oil, gossypol content are 3-1,3-3, and 4-2, respectively. And the variation explained are 2.42%～23.04%. These QTLs detected for seed quality traits in cotton are expected to be useful in the breeding program for cottonseed nutrient quality.
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