Breeding Effects and Genetic Compositions of a Backbone Parent (Fengbazhan) of Modern indica Rice in China

Zhao Lei, Zhou Shaochuan, Wang Chongrong, Li Hong, Huang Daoqiang, Wang Zhidong, Zhou Degui, Chen Yibo, Gong Rong, Pan Yangyang

Letter

Breeding Effects and Genetic Compositions of a Backbone Parent (Fengbazhan) of ModernRice in China

Zhao Lei, Zhou Shaochuan, Wang Chongrong, Li Hong, Huang Daoqiang, Wang Zhidong, Zhou Degui, Chen Yibo, Gong Rong, Pan Yangyang

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Fengbazhan (FBZ) andits derived varieties have been widely cultivated in China, accounting for 22% of China’s paddyfields.Therefore, evaluating the breeding. Effectsof FBZ and elucidating its genetic compositions are effective strategies for interpreting the history of modern rice breeding.Using integrative bioinformatics analysis and population validation,we found that the expression of favorable genes on chromosome 6 was important for the breeding of FBZ-derived varieties and these favorable genes were gradually optimized during thebreeding process, which was consistent with the conjecture of the ‘Rice Core Germplasm Breeding Theory’.

Forseveral decades, tremendous efforts have been made by Chinese scientists in rice breedingto improvegrain yield, nutritional quality and environmental performance, thereby achieving substantial progress in globalfood security.Several rice breeding technologies have been developed, includingsemi-dwarf breeding, utilization of heterosis, launching the ‘Super Rice Project’, development of green super rice and molecular design breeding(Qian et al, 2016;Bai et al, 2018; Tang and Cheng, 2018; Yu et al, 2022).In southern China, rice can be divided into the early, middle and late rice, andthe cultivationarea in southern China accounts for approximately80% of China’s rice cultivation area.Currently, severaldistinct rice varieties are widely cultivated in southern China. According to NATESC (2019), the conventionalrice variety is mainly planted in the early season,with therepresentative varieties being Zhongjiazao17, Xiangzaoxian45 and Zhongzao39. In the middle and late seasons, both conventionaland hybrid rice varieties are widely cultivated. Among them, Huanghuazhan has become the conventionalrice variety with the largest annual planting area in China, whereasJingliangyou534 (restorer: Wushansimiao) and Jingliangyou- huazhan (restorer: Huazhan) are the two-hybrid rice varieties with the largest annual promotion area.In addition, Huanghuazhan and Huazhan are actively replacing the rice varieties currently usedin China(Zhou et al, 2016; Zeng, 2018; E et al, 2019; Fang et al, 2020; Yu et al, 2022; Zhang et al, 2022).Moreover, these varieties are derived from FBZand can therefore be referred toasFBZ-derived varieties.

FBZ was developed by crossing two key parents, Feng’aizhan1 and 28zhan (Fig. 1-A).Feng’aizhan1 is a semi-dwarf rice variety with multiple tillers, high yield and slender grains, but it exhibits poor blast resistance and has high amylose content.In contrast, 28zhan exhibits excellent blast resistance and has low amylose content, although its appearance quality and grain yield are not ideal.FBZ inherits the advantages of both parents (Zhou et al, 2007), and thus, itis a remarkable rice variety exhibiting excellent milling, appearance and cooking qualities,blast resistance, and high yield in Guangdong Province in China.Our team used FBZ as the core germplasm to breed the first certified rice variety Fenghuazhan (Fig. 1-A). The appearance and taste quality of Fenghuazhan were significantly improved compared to those of FBZ. Subsequently, our team bred another elite rice variety Huanghuazhan, by crossing Huangxinzhan and Fenghuazhan, which was released in 2005 (Fig. 1-A).Huanghuazhan is the most common inbred rice cultivar that has been cultivated in central and south China and has been widely grown across nine provinceswith semi-dwarf,super high yield,good eating qualityand wide adaptability(Zhou et al, 2016; Deng et al, 2019). Nevertheless, Huanghuazhan exhibits a significantly reducedblastresistance compared to FBZ, which may limit its application in areas with a high risk of rice blast. To overcome these limitations, we developed two intermediary varieties, Wufengzhan2 and Fengsizhan, which were directly derived from FBZ. Based on these two varieties, Wushansimiao, Huanglizhan,and Huangyuesimiao were bred by our institute and Huazhan was cooperatively bred by our institute and China National Rice Research Institute (Fig. 1-A), and thesefour varieties have proven to be elite restorer lineswith good quality, high blast resistance and excellent combining ability. The breeding and popularization of hybrid rice were mainly completed by our partners, namely the China National Rice Research Institute, Longping High-TechAgriculture Co., Ltd.,and Quanyin High-TechSeed Co., Ltd.

Fig. 1. Breeding effects of Fengbazhan (FBZ) in China.

A, FBZ-derived varieties bred by our team. Huazhan was cooperatively bred by our team and China National Rice Research Institute. Seven elite varieties are shown in boxes.B, Planting areas of FBZ-derivedvarieties in China. C, Main locations whereFBZ-derivedvarieties are cultivated in China.D,Percentage of the planting area of FBZ-derived hybrids with respect tothe total planting area of hybrid rice in China. The unit is × 104hm2. E, Percentage ofplanting area of FBZ-derived varieties (including hybrid rice and conventional rice) with respect tothe total rice areain China (NATESC, 2019). The unit is × 104hm2.F, Released FBZ-derived conventional rice varieties in Guangdong Province of China from2000 to 2020.

The promotion of FBZ-derived varieties began in 2002, and theirplantingarea has increased dramatically since2009.The maximum planting area ofconventional rice derived from FBZwas recordedin 2015, whereasthe area of FBZ-derived hybrid rice has been rapidly increasing in recent years (Fig. 1-B).Geographically, therice variety is mainly distributed in the south of the Huai River-Qinling Mountain line. Fig. 1-C shows thatthe FBZ-derived varieties have been widely cultivated in all therice-growing areas of China. In 2019, 79 hybrid rice varieties derived from the FBZ-series restorer lineswere promoted for production in 3 806 000 hm2,accounting for 35% ofthe total hybrid rice planting area in China (Fig. 1-D). In addition to hybrid rice, 10 conventional FBZ-derived varieties havebeen sowed. In general, the planting area for FBZ-derivedvarietiesaccounts for 22% of the total rice planting area in China (Fig. 1-E). Shanyou63, a milestone in China’s hybrid ricedevelopment, had a large planting area from 1985 to2001, with an average area of 3.6 million hectaresand 28.3% of the national hybrid rice-growing areas annually(Xie and Zhang, 2018).The annual planting area of FBZ-derived hybridsexceeded that of Shanyou63.Additionally, more than 90% of the conventional rice varieties released in Guangdong Province in recent years are descendants of FBZ(Fig. 1-F), indicating that FBZ has become the backbone parent of conventional rice varieties and the development of FBZ can be regarded as a milestone in modernrice breeding in China.

We collected the genomic data of 138 varieties to reveal the genetic basis of the FBZ-derived varieties (Table S1). Population structure analysis showed that the genetic distances of the iconic restorer lines were generally close, whereas the FBZ-derived varieties showed separate clustersand were closest to the elite conventional ricevarieties (Fig. 2-A). In China, the maleparents of hybrid rice varieties are either imported directly from the International Rice Research Institute (IRRI) or developedusing IRRI varieties as donor parents (Xie and Zhang, 2018), which means most of the restorer lines share more than 40% ancestry from IRRI varieties. In contrast, only 25% ancestry of FBZ is derived from IRRI varieties and is even less in FBZ-derived varieties (Fig. 1-A). We speculated that the close genetic distance between elite conventional rice and the FBZ-derived varieties is an important reason for their wide adaptability and high yield, while the ancestry from IRRI variety allows FBZ to acquire fertility restoration and rice blast resistance, which can explain why FBZ-derived varieties can be used as conventional rice and as restorer lines.

Fig. 2. Geneticfeatures of varieties derived from Fengbazhan (FBZ).

A, Neighbor-joining tree of138 varieties. B, Inheritance pattern of chromosome 6 in thebreeding of the latest FBZ-derived varieties. Genotypes were drawn based on penta-primer amplification refractory mutation markers. Genes contributing tomodernrice varieties are marked on the top. White (FBZ) and red (others)bars denote the parental origin of the segments. Haplotypes of,andloci were marked with arrows.C, Allelic effects oflocus on the entire growth duration. D, Effects ofallelic diversity on AC. G1,wxvarieties (= 14); G2,wxvarieties (= 26); G3,varieties (= 67). E–G, Effects oflocus on Zhong B (E), Zhong C (F), and total (G)groups of the blast fungus. G-I, +++varieties (= 67); G-II, +--varieties (= 7); G-III, ---varieties (= 19). AC, Amylose content; RF, Resistance frequencyto total rice blast fungus in GuangdongProvince, China. Different lowercase letters denote significant differences (< 0.05).

By comparing the variant information of 222 genes that are responsible for quantitative traits (QTGs)(Wei et al, 2021), we identified 48 QTGs exhibiting allelic differences among rice varieties (Fig. S1).Among them, 10 QTGswere differentially used betweenGroup I (landraces) and Group II (landmark semi-dwarf varieties), and 33 QTGsunderwentartificial selection between Group II and Group III (iconic restorer lines / conventional rice),and 4 QTGs (,,and) wereexclusively used in Group IV (FBZ-derived varieties) (Fig. S1). These findingsindicated that 91.6%of the QTGs wereselected before FBZ was bred,whereas only a few QTGsdirectly contributed to the breeding of FBZ-derived varieties.

Remarkably, the four QTGs (,,and) weretandemly distributed on chromosome 6.Moreover, 8 of the 48 QTGs werelocated on chromosome 6, and together they accounted for 25% of the 48 QTGs(Fig. S1).Among them, several genes play an important role in rice breeding. For example,andare major genes responsible foreating and cooking quality(Tianet al, 2009), whileaffects both lodging resistance and productivity(Ookawa et al, 2010). We noticed thathas no functional variation in Group IV as compared to the other groups, while causative variantscorresponding toalso existed in the other groups. Sequence alignment analysis revealed that the FBZ-typeallele was different compared to the other widely promoted varieties, such as Minghui63 and 9311. Compared withNipponbare, Huazhan has two single nucleotide polymorphisms(SNPs) and one base deletionin the coding region (Fig. S2-A), and the FBZ haplotype was the closest to theWxallele (Fig. S2-B). By comparing the gene sequences ofthe four tandem genes, we found that thesequences ofandof Huazhan were identical to those of C101A51 (-carrying line) and Gumei2 (-carrying line)(Fig. S3-A and -B). We observed only one SNP in thegenebetween Huazhan and Digu (-carrying line) (Fig. S3-C), but this variant does not exist in both Ricevarmapand Rice RC databases (Zhao et al, 2015; Qin et al, 2021), indicating that the SNP in Digu (GenBank: FJ915121.1) is caused by sequencing errors. Hence, Huazhan also carried the resistance allele of.For, both Huanghuazhan andMinghui 63 harbored a 4-bp frameshift deletionat the 1 904bp position, while Huazhan harbored a 2-bpframeshift deletionat the 1 686 bp position(Fig. S4).Given that hundreds of conventional rice varieties have been derived from FBZ,we speculated how these 12 QTGswere inherited in the latest FBZ-derived varieties. We collected DNA samples from176rice varieties (Table S2). According toPARMS (penta-primer amplification refractory mutation) genotyping (Lu et al, 2020), the 83 FBZ-derived varieties can be divided into 13 groups. Surprisingly, 64 of the 83 varietiesshared the same genotype at locusChr6: 1.6–23.3 Mb, except for the variation in thelocus (Fig. 2-B).This finding strongly indicated that most of the beneficial QTGs on chromosome 6 were inheritedduring the breeding of FBZ-derived varieties.

Considering the influence of,,,andon agronomic traits, we extracted data on the amylose content, whole growth period, and rice blast resistance from varietiescertification announcements. Compared to(Huanghuazhan- type), the whole growth period of(Huazhan-type, which exists in most FBZ-series varieties) showed no significant difference in the early or late seasons (Fig. 2-C), which indicated that the variation inhaplotype did not influence its gene effect in FBZ-series varieties.For, 75.9% of the FBZ-series varieties contained theallele, while varieties carrying theWxallele accounted for 22.9%.There was no significant difference inamylose content betweentheand Wxvarieties, however, their amylose content was significantly lower than that oftheWxvarieties(Fig. 2-D).This patternindicated thatwas also a favorable allele for rice quality improvement. We identifiedsix genotype combinations of,andin 176 varieties.The varieties carrying theresistance allele can significantly improvethe frequency of resistance toZhong B, Zhong C,and total group of rice blast fungus, as well as the comprehensive resistance to rice blast.Nevertheless,andhad little effect on blast resistance in this study (Fig. 2-E to -G). Taken together, the utilization of the favorable genes on chromosome 6 removed the problem of ‘highquality butlow blast resistance’, enabling the FBZ-derived varieties to achieve a high and stable yield, good quality and wide adaptability in production.

To identify the favorable genes involved inthe breeding process of the FBZ-derived varieties, we compared the allelic differences of 222QTGs between the FBZ-derived varieties and their ancestors. A total of 16 QTGs, with beneficial functions inFBZ-series varieties, were identified as key candidate genes according to functional variation information. These 16 QTGs were included in the 48 QTGs that showed haplotype differences among different varieties, except for. The 16 QTGs arewell-known important functional genes,which allowed us to understand their genetic effects.These QTGs had distinctivecharacteristics of gradual replacement, and they were mainly selected at fourstages (Fig. S5). Firstly, five QTGs were selected during the semi-dwarf breeding period, inducingthe variety Teqing to exhibit semi-dwarf (), delayed heading (), partial fertility recovery (),and compact plant type (and) properties. Secondly, six QTGs were integrated to breedQingliuai1, including genes related to fertility restoration (and), grain protein content (), blast resistance (), and bacterial blight resistance (and). Thirdly, Feng’aizhan1 utilized three QTGs (/,and), thereby exhibiting a slender and chalk-free appearance.Lastly, two QTGs were used to breed FBZ, making it possible to breed varieties withlow amylose content () and highresistance to rice blast ().Favorable genes were gradually optimized during thebreeding of FBZ-series varieties, which was consistent with the conjecture of the ‘Rice Core Germplasm Breeding Theory’(Zhou and Ke, 1998; Zhou et al, 2021).

Our team also bred another iconic aromatic rice variety Meixiangzhan2, which is the onlyrice variety and has won three gold medals awarded by thenational committee for evaluation ofthe eating quality of high-quality rice varieties, and its taste quality has surpassed Thai Hom Mali Rice KDML105.Meixiangzhan2 was released in 2006 and has been widely planted in China, with an annual promotion area of approximately 133000 hm2(NATESC, 2019).It has also been introduced to Myanmar, Vietnam, Laos, Thailand, Mozambique, and other countries for cultivation(Li et al, 2021). In the future, we will work on breeding a variety that has highyield, disease resistance properties, and combining the ability ofthe FBZ-derived varieties with the eating quality of Meixiangzhan2.To achieve this goal, some favorable genes,such as,,,and, could be manipulatedusing molecular marker-assisted selection technology to improve breeding efficiency.In addition, it is necessary to introduce more germplasm resources, especially for theorrice variety, todiscover more favorable alleles or combinations of favorable genes, thereby creating a new balance between yield, quality and resistance.

In conclusion, we systematically analyzed the breeding effects and genetic characteristics of FBZ.We determinedthat the genetic composition of the FBZ-derived varieties is distinctfrom that of the other restorer lines.Our research demonstrated that the improvement in rice varieties was essentially a trajectory of gradual optimization from the original system to the ideal gene system. Notably,breakthrough varieties are often bred using only a few genes or chromosomal segments.We believe that our findings will provide important references for rice breeding.

Acknowledgements

This study was supported by the Laboratory of Lingnan Modern Agriculture Project (Grant No. NT2021001), Applied Science and Technology of Guangdong Province, China (Grant No. 2015B020231001), Guangdong Academy of Agricultural Sciences Agricultural Advantage Industry Discipline Team Building Project (Grant No. 202111TD): Quality Rice Core Germplasm Breeding Team (2021–2025), Special Fund for Science and Technology Innovation Strategy of Guangdong Academy of Agricultural Sciences: Dean’s Fund Key Project (Grant No. 202001), Collection and Evaluation of High-Quality Germplasm Resources of ‘Guangdong Simiao Rice’ (Grant No. 2021KJ382-02) and Operating Fees for Key Laboratory of Guangdong Province (Grant No. 2020B1212060047). We thank Mr. Gu Minghong from Yangzhou University for his valuable comments and suggestions and Professor Liang Wanqi from Shanghai Jiaotong University for providing seeds of several ancestral varieties of Fengbazhan.

Supplemental data

The following materials are available in the online version of this article at http://www.sciencedirect.com/journal/rice-science; http://www.ricescience.org.

File S1. Methods.

Fig. S1. Allele types of causatice variants involved in Chinese modernrice breeding.

Fig. S2. Sequence features of FBZ-type allele in coding regions ofgene.

Fig. S3. Sequence analysis of,andin Huazhan.

Fig. S4. Sequence features ofin Huazhan and Huanghuazhan.

Fig. S5. Genes flow of key candidate genes involved in breeding of FBZ-derived varieties.

Table S1. List of rice accessions used for variant information extraction in this study.

Table S2. Genotyping of 10 loci in 176 rice varieties using penta-primer amplification refractory mutation markers.

Bai S W, Yu H, Wang B, Li J Y. 2018. Retrospective and perspective of rice breeding in China., 45(11): 603–612.

Deng N Y, Grassini P, Yang H S, Huang J L, Cassman K G, Peng S B. 2019. Closing yield gaps for rice self-sufficiency in China., 10(1): 1725.

E Z G, Cheng B Y, Sun H W, Wang Y J, Zhu L F, Lin H, Wang L, Tong H H, Chen H Q. 2019. Analysis on Chinese improved rice varieties in recent four decades., 33(6): 523–531. (in Chinese with English abstract)

Fang Y W, Zhang W, Chen Y Y, Hou F, Xu L F, Tang C H, Li R D. 2020. State quo of utilization of high-quality hybrid rice varieties in China during 2001–2017., 32(1): 1–14. (in Chinese with English abstract)

Li H, Zhou S C, Huang D Q, Wang Z D, Wang C R, Zhou D G, Chen Y B, Gong R, Zhao L, Pan Y Y. 2021. The breeding and enlightenment of Meixiangzhan 2, a aromatic rice variety with good eating quality., 39(2): 1–6. (in Chinese with English abstract)

Lu J, Hou J, Ouyang Y D, Luo H, Zhao J H, Mao C, Han M, Wang L, Xiao J H, Yang Y Y, Li X. 2020. A direct PCR-based SNP marker-assisted selection system (D-MAS) for different crops., 40(1): 1–10.

National Agricultural Technology Extension Service Center (NATESC). 2019. Statistics on the Promotion of the Main Varieties of Crops in 2019. Beijing. (in Chinese)

Ookawa T, Hobo T, Yano M, Murata K, Ando T, Miura H, Asano K, Ochiai Y, Ikeda M, Nishitani R, Ebitani T, Ozaki H, Angeles E R, Hirasawa T, Matsuoka M. 2010. New approach for rice improvement using a pleiotropic QTL gene for lodging resistance and yield., 1: 132.

Qian Q, Guo L B, Smith S M, Li J Y. 2016. Breeding high-yield superior quality hybrid super rice by rational design., 3(3): 283–294.

Qin P, Lu H W, Du H L, Wang H, Chen W L, Chen Z, He Q, Ou S J, Zhang H Y, Li X Z, Li X X, Li Y, Liao Y, Gao Q, Tu B, Yuan H, Ma B T, Wang Y P, Qian Y W, Fan S J, Li W T, Wang J, He M, Yin J J, Li T, Jiang N, Chen X W, Liang C Z, Li S G. 2021. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations., 184(13): 3542–3558.

Tang D, Cheng Z K. 2018. From basic research to molecular breeding: Chinese scientists play a central role in boosting world rice production., 16(6): 389–392.

Tian Z X, Qian Q, Liu Q Q, Yan M X, Liu X F, Yan C J, Liu G F, Gao Z Y, Tang S Z, Zeng D L, Wang Y H, Yu J M, Gu M H, Li J Y. 2009. Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities., 106(51): 21760–21765.

Wei X, Qiu J, Yong K C, Fan J J, Zhang Q, Hua H, Liu J, Wang Q, Olsen K M, Han B, Huang X H. 2021. A quantitative genomics map of rice provides genetic insights and guides breeding., 53(2): 243–253.

Xie F M, Zhang J F. 2018. Shanyou 63: An elite mega rice hybrid in China., 11(1): 17.

Yu S B, Ali J, Zhou S C, Ren G J, Xie H A, Xu J L, Yu X Q, Zhou F S, Peng S B, Ma L Y, Yuan D Y, Li Z F, Chen D Z, Zheng R F, Zhao Z G, Chu C C, You A Q, Wei Y, Zhu S S, Gu Q Y, He G C, Li S G, Liu G F, Liu C H, Zhang C P, Xiao J H, Luo L J, Li Z K, Zhang Q F. 2022. From green super rice to green agriculture: Reaping the promise of functional genomics research., 15(1): 9–26.

Zeng B. 2018. Renovation of main cultivated rice varieties in China in the past 30 years., 34: 1–7.

Zhang H, Wang Y X, Deng C, Zhao S, Zhang P, Feng J, Huang W, Kang S J, Qian Q, Xiong G S, Chang Y X. 2022. High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan., 65(2): 398–411.

Zhao H, Yao W, Ouyang Y D, Yang W N, Wang G W, Lian X M, Xing Y Z, Chen L L, Xie W B. 2015. RiceVarMap: A comprehensive database of rice genomic variations., 43: D1018–D1022.

Zhou D G, Chen W, Lin Z C, Chen H D, Wang C R, Li H, Yu R B, Zhang F Y, Zhen G, Yi J L, Li K H, Liu Y G, Terzaghi W, Tang X Y, He H, Zhou S C, Deng X W. 2016. Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding., 14(2): 638–648.

Zhou S C, Ke W. 1998. Talking about the excellent germplasm and its derivative system in breeding., (Suppl): 1–5. (in Chinese)

Zhou S C, Li H, Zhu X Y, Miao R W, Lu D C, Zeng L X, Huang D Q, Lai S C, Li K H. 2007. Breeding of Fengbazhan and its derivative varieties and comprehensive analyses of the breeding achievement: The case of rice core germplasm breeding., (5): 5–11. (in Chinese with English abstract)

Zhou S C, Ke W, Miao R W, Li H, Huang D Q, Wang C R. 2021. Creation and application of the breeding theory based on rice core germplasm., 35(6): 529–534. (in Chinese with English abstract)

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