’Junks’ help improve new rice varieties

Junks may not be totally useless if something is done to make them beneficial to man.

One good example is the improved IR58025B where the IRBB lines of IRRI (International Rice Research Institute) were used as bacterial blight resistance gene donor.

Intended as the hybrid maintainer parent of the hybrid Mestizo 1, IR58025B should be used to reproduce its sterile counterpart, the cytoplasmic male sterile (CMS) or female IR58025A, which is used to produce the Mestizo hybrid rice variety. In other words, the improved IR58025B line is expected to maintain the sterility of IR58025A line.

However, highly fertile plants were produced when the improved IR58025B was crossed with IR58025A. Offsprings of the cross were expected to be sterile, but they were highly fertile.

Consequently, other researchers no longer used the improved IR58025B as hybrid maintainer parent even as it already possessed the BLB (bacterial leaf blight) resistance genes Xa4, Xa7 and Xa21, which were earlier incorporated into it through conventional backcross breeding.

PhilRice senior science research specialist Joan Agarcio said the improved IR58025B should serve as the donor of the BLB resistance genes Xa4, Xa7 and Xa21 to its female IR58025A counterpart in order to eventually incorporate these genes in hybrid rice seeds. So she wanted to find out what was wrong with IR58025B.

Before Agarcio started her research on this problem, the Mestizo parents and hybrids were susceptible to BLB and, hence, extensive use of IR58025A over a large production area presents a potential problem of vulnerability to insect pests and diseases.

Unlike conventional inbred varieties, rice hybrids are more responsive to nitrogenous fertilizer and exhibit vigorous growth. These attributes have made most of the rice hybrids susceptible to BLB, which can cause up to 50 percent yield loss especially during the wet season when the plants are predisposed to the bacteria.

The susceptibility of hybrid parents is aggravated by the cultural practice of flag leaf clipping by farmers during hybrid rice seed production. This practice creates wounds, which become entry points for the bacteria.

Working on this problem for her master’s thesis, Agarcio had to determine where the problem was. She found out that "near isogenic lines" or NILs of IR24, which were developed by IRRI a long time ago, were used as BLB resistance donors.

She discovered that the IR24 background of the IRBB donors for BLB resistance contained two dominant restorer genes — Rf3 and Rf4, which were reported to be responsible for restoring fertility in the wild-abortive type CMS cytoplasm of IR58025A. "This explains why the offspring are fertile when they should be sterile," Agarcio said.

Next, she looked for genetic markers linked with Rf3 and Rf4. The only available marker at that time was for Rf3, but IRRI came up with the marker for Rf4 right on time when she was about to start her study. These markers are needed so she can determine the presence or absence of the two Rfs in the advance progenies before she could select and refine those with the Xa resistance genes but without the two Rfs.

She checked the advanced progenies whether the Xa resistance genes were really there as well as the presence of the two Rfs. Different combinations came out, but she only retained the plants with the three BLB resistance genes and without the two fertility restorer genes. She discarded all other plants — those with Rf3 and Rf4 even if they had the three BLB resistance genes — because they could not be used for breeding.

She used two types of selection — one for the resistance genes and another for the fertility restorer genes — and screened the materials hoping to come up with true-to-type B lines that would maintain the sterility of the A lines.

Agarcio "fingerprinted" her selections and compared them with the original A and B lines using two markers, which are called resistance gene analogs or RGA markers. The latter are said to spread out throughout the rice genome, thereby covering its 12 chromosomes.

This increased her chances of covering the 12 rice chromosomes with the markers generating multiple bands. The bands generated by the offspring and those by the parents showed how similar the improved progenies were with the original parents.

At most 91 percent of the parental traits were found in the progenies at BC4F1 (fourth backcross first generation). Theoretically, it is expected that the recovery should be 96 percent.

In effect, what was initially considered as junk turned out into a very valuable asset. Further work on it also became an award-winning research.