Typing of Inter-subspecific Fertility Loci and Fertility Locus Pattern of indica-japonica Hybrid Rice

doi:10.16819/j.1001-7216.2024.230801

Abstract

Abstract:

【Objective】 The objective of this study is to investigate the distribution of inter-subspecific fertility loci in indica rice, japonica rice, and indica-japonica hybrid rice in China. This involves establishing a pattern of fertility loci to achieve compatibility between different subspecies, exploring new indica-japonica hybrid rice patterns, and laying a molecular basis for improving materials and breeding designs for inter-subspecific compatibility.【Method】 Specific markers for indica and japonica rice were used to screen for inter-subspecific fertility loci in rice materials from China. Several indica and japonica rice varieties were crossed with each other, and the pollen fertility and seed setting rate of the resulting hybrids were statistically analyzed.【Results】 There was limited genetic exchange between indica and japonica rice at the fertility loci. Due to introgression of fertility loci from indica rice, japonica rice could be classified into type I (pure japonica) and type II (with introgressed indica loci such as Scⁱ, Sdⁱ, and Seⁱ). When S5 was incompatible, the seed setting rate of inter-subspecific hybrid rice was approximately 50%, while it increased to about 80% when compatible. Heterozygosity at Sa, Sb, Sc, or Sd loci had minimal impact on pollen fertility, but heterozygosity of Se/pf12/RHS12 significantly reduced it. The detection results of inter-subspecific hybrid rice materials indicated that the basic fertility loci pattern was homozygous or compatible S5 along with several other fertility loci for pollen fertility. The pollen fertility and seed setting rate of F₁ hybrids from the indica two-line male sterile line Shen 08S with S5ⁿ and japonica type II rice were normal.【Conclusion】 SS5 is the core locus controlling female gamete fertility, while loci affecting male gamete fertility have an additive effect. Se may be an indispensable locus among them. The possible basic genetic locus patterns for achieving fertility compatibility between indica and japonica subspecies include S5+Se+two other loci among Sa, Sb, Sc, and Sd. The ‘maternal indica paternal japonica’ model, utilizing two-line indica rice male sterile lines with wide compatibility as female parents and japonica rice as male parents, presents another feasible inter-subspecific hybrid rice model.

Key words: inter-subspecific fertility loci, typing, inter-subspecific hybrid rice, fertility locus pattern

摘要：

【目的】 了解我国籼稻、粳稻材料及籼粳杂交稻组合中亚种间育性位点的分布，建立实现亚种间育性亲和所需遗传位点模式，探索新的籼粳杂交稻组合模式，为亚种间亲和材料改良和籼粳育性亲和分子设计育种打下基础。【方法】 通过筛选得到育性位点的籼粳分型标记对我国水稻材料进行育性位点的籼粳分型检测，挑选部分籼稻、粳稻亲本进行杂交并统计分析F₁代花粉育性和结实率。【结果】 籼稻和粳稻之间在所有育性位点均存在少量相互渗入。由于籼稻育性位点渗入，粳稻可以分为Ⅰ型（所有位点均为粳型）和Ⅱ型（Scⁱ、Sdⁱ和Seⁱ，上标i代表来自籼稻）。S5不亲和时籼粳杂交稻结实率约为50%，亲和时结实率约为80%。Sa、Sb、Sc或Sd单个位点杂合对于花粉育性影响较小，但Se/pf12/RHS12单个位点杂合时显著降低花粉育性。籼粳杂交稻材料检测结果表明其育性位点的基本模式是S5和部分花粉育性位点纯合/亲和。带有S5ⁿ的籼稻两系不育系深08S与粳稻Ⅱ型材料的杂交F₁代的花粉育性和结实率正常。【结论】 S5是控制雌配子育性的核心位点。影响雄配子育性的位点具有累加效应，其中Se可能是不可缺少的重要位点。S5+Se与Sa、Sb、Sc、Sd任意两个纯合位点可能是实现籼粳亚种间育性亲和的基本遗传位点模式。以广亲和两系籼稻不育系为母本，常规粳稻为父本的“籼不粳恢”籼粳杂交模式是一个可行的亚种间组合模式。

关键词: 亚种间育性位点, 分型, 籼粳杂交稻, 育性位点模式

CHEN Mingliang, ZENG Xihua, SHEN Yumin, LUO Shiyou, HU Lanxiang, XIONG Wentao, XIONG Huanjin, WU Xiaoyan, XIAO Yeqing. Typing of Inter-subspecific Fertility Loci and Fertility Locus Pattern of indica-japonica Hybrid Rice[J]. Chinese Journal OF Rice Science, 2024, 38(4): 386-396.

陈明亮, 曾细华, 沈雨民, 罗世友, 胡兰香, 熊文涛, 熊焕金, 吴小燕, 肖叶青. 籼粳亚种间育性位点分型及籼粳杂交稻育性位点模式研究[J]. 中国水稻科学, 2024, 38(4): 386-396.

Figures/Tables 8

Table 1. Information of molecular markers used in detection for fertility loci in the present study

位点Locus	引物名称 Primer name	前引物 Forward primer	后引物 Backward primer	文献Reference
S5	ORF3-S513	ACCCACCTTGGTTCATCGTC	TTCCCGTCCTCTACCTGTTG	[14]
	ORF4-S5P50	GAACACCTCGAATAAGCT	CTGCTGCCTCTGTGTCTA	[14]
	ORF5-S5W*	GCCATTCCTTCCGATAT	GTGCTTTGCTACTTACCG	[14]
S31	Ind229	TAGCAAATTCCATGAAGT	CTGAAGAACCAGTCGTAG	[15]
Sa	G02-69	TGTGCACTCGTCTCTCATCT	GGTGGTGAAGAGAGGCTTG	[16]
Sb	A755	GCAGTTACCGGCAACGAGG	GACTGACCCCTACCACCAC	[17]
	LInD5-165	TGCTTAGTGTACTGTTTGCGGT	GTAATTGGGCTTCGTGGTGACC	[18]
Sc	84.7	ACAAAGCAAATAGGAGAT	CGTGGCCGCACTTGCTAC	[19]
	93	GCTTCGCTCCCGTCATCATC	ACAACTCCAGTAAGAACTCC	[19]
Sd	Ind3	CGGTCAGGTTTGAGTAGTTGC	ATTGTTGGCTAAGCCATGCTA	[20]
Se	IND31	CCCTACAACTAATGCAGGTTCAG	GGACCCTTACGCCATTGATC	[21]
HSA1	M231	GGATATTTGCTCTGCTGCAA	TGGTGTCGCCACCTTTCTTC	[22]
	M914	TGACGTTCCTTTTGGGTTTT	GCTGGAGTGCTTTGGTGATT	[22]
HSA2	LInD8-256	TCTAAGAAAGTCAGGCACCCCG	TCATCGAACCCTTGCACTCTGA	[18]
HSA3	LInD9-188	GCTTGAGAGCTCCATCGTTTACT	TGTTCAAATCCTGTTGCGATGGT	[18]
DPL1	C6342	GAATATTTGGGAGCCCCTGT	TGTTAAAAGGAGGCGCACTT	[23]
DPL2	C3815	TCTGGGCCAAATTTGACTGT	TTTGTTCTGCATTCCCTCCT	[23]

Table 2. indica/japonica typing of inter-subspecific fertility loci for the tested rice materials in the present study

分类 Type	S5				S31				Sa						Sb					Sc
分类 Type	籼i	粳j	广亲和n		籼i		粳j		籼i		粳j		广亲和n		籼i		粳j			籼i		粳j
粳稻japonica	4	189	4		3		194		0		197		0		2		195			106		91
籼稻indica	209	0	7		214		2		202		10		4		210		6			216		0
粳型不育系japonica CMS	1	8	0		0		9		0		9		0		0		9			9		0
粳型恢复系japonica RL	1	3	11		4		11		10		5		0		4		11			14		1
广亲和材料 Wide compatibility material	0	0	4		1		3		1		3		0		1		3			3		1
总计Total	215	200	26		222		219		213		224		4		217		224			348		93
分类 Type	Sd		Se			HSA1				HSA2				HSA3				DPL1			DPL1*
分类 Type	籼i	粳j	籼i	粳j		籼i		粳j		籼i		粳j		籼i		粳j		籼i	粳j		籼i		粳j
粳稻japonica	85	112	90	107		0		197		18		179		2		195		0	197		5		192
籼稻indica	208	8	214	2		193		23		213		3		211		5		16	200		207		9
粳型不育系japonica CMS	9	0	9	0		0		9		0		9		0		9		0	9		0		9
粳型恢复系japonica RL	14	1	10	5		11		4		13		2		10		5		1	14		14		1
广亲和材料 Wide compatibility material	0	4	1	3		0		4		3		1		1		3		0	4		2		2
总计Total	316	125	324	117		204		237		247		194		224		217		17	424		228		213

Fig. 1. Phylogenetic analysis of indica/japonica inter-subspecific fertility loci in rice A, Phylogenetic tree of inter-subspecific fertility loci in partial rice accessions; B, Phylogenetic tree of inter-subspecific fertility loci in part japonica rice accessions. Different colors indicate different types or planting area of rice accessions, and gray circle represents different clusters.

Fig. 2. Effect analysis of inter-subspecific fertility loci that control female gamete fertility in rice A, Effect on seed setting rate of S5 and S31 under normal pollen fertility. Different lowercase letters mean significant difference (P < 0.05). Sample numbers were 87, 25, 9, 80 and 6, respectively; B, Correlation analysis between seed setting rate and normal pollen rate.

Fig. 3. Effect analysis of inter-subspecific fertility loci that control male gamete fertility in rice A, Pollen fertility and seed setting rate of different male gamete loci combinations under S5 compatibility; Sample numbers were 8, 6, 16, 7, 32, 22 and 6, respectively. B, Pollen fertility and seed setting rate of different male gamete loci combinations under S5 incompatibility. Sample numbers were 27, 6, 8, 26, 7 and 7, respectively. Different lowercase letters mean significant difference (P < 0.05). The five numbers on the horizontal axis represent the indica-japonica classification of the Sa, Sb, Sc, Sd, and Se loci, where 1 represents the indica type, 2 represents the japonica type, 3 represents the heterozygous type, and n represents a wide compatibility allele.

Fig. 4. Analysis of fertility loci that control male gamete fertility in japonica rice from different areas. The number represents the percentage of tested accessions for the genotype in this study.

Fig. 5. Pollen fertility and seed setting rate in hybrids from crossing different japonica rice Pollen scale bars, 100 μm.

Fig. 6. Pollen fertility and seed setting rate in hybrids from crossing Shen 08S with different rice types Pollen scale bars, 100 μm.

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